UNIT-1

Microbiology Definition

Microbiology is the study of microscopic organisms, such

as bacteria, fungi, and protists. It also includes the study of viruses,
which are not technically classified as living organisms but do
contain genetic material. Microbiology research encompasses all
aspects of these microorganisms such as their behavior,
evolution, ecology, biochemistry, and physiology, along with
the pathology of diseases that they cause.

History of Microbiology

Scientists first observed microorganisms when the first primitive

microscopes were developed during the 17th Century. Anton von
Leeuwenhoek was the first to publish observations of bacteria,
which he viewed by looking at water with a microscope. In 1684,
his drawings of bacteria were published in the Royal Society of
London’s journal Philosophical Transactions; these are the first
known drawings of bacteria. He was also first to describe protozoa,
which are single-celled organisms that include amoebae, and also
described yeast, which are fungi, in beer.

Microbiology techniques used to disprove the long-held theory

of spontaneous generation in the 19th Century. Spontaneous
generation was the belief that living things arose spontaneously
from a combination of ingredients, often including ingredients that
were inorganic. For example, people believed that mice arose from
soiled cloth combined with wheat if the combination was left out to
sit. Although scientists such as Francesco Redi had disproven
spontaneous generation as early as the 17 th Century, belief in the
theory persisted up to the 19th Century. This started to change
when Louis Pasteur conducted experiments using microorganisms.
He showed that microorganisms could be filtered out of air by using
cotton wool, and he was also able to keep liquids sterile for an
extended period of time by boiling them in a swan-necked flask.
Other important advancements in the 19 th Century included the
widespread use of the compound microscope and the development
of staining techniques in order to better visualize microorganisms.
In addition, people began to realize that microorganisms could
cause disease, and did experiments on immunity.

The 20th Century was a time of great advancement for all forms of
science, including microbiology. The first vaccines and antibiotics
were developed, and the first chemotherapeutic agents were used
to treat bacterial diseases such as syphilis. Deoxyribonucleic acid
(DNA) was discovered to be the genetic material of the cell, which
opened up the field of genetics research and allowed more recently
for sequencing the genomes of microorganisms.

Branches of Microbiology

By Taxonomy

 Bacteriology: the study of bacteria.

 Immunology: the study of the immune system. It looks at the

relationships between pathogens such as bacteria and viruses
and their hosts.
  Mycology: the study of fungi, such as yeasts and molds.

 Nematology: the study of nematodes (roundworms).

 Parasitology: the study of parasites. Not all parasites are

microorganisms, but many are. Protozoa and bacteria can be
parasitic; the study of bacterial parasites is usually categorized
as part of bacteriology.

 Phycology: the study of algae.

 Protozoology: the study of protozoa, single-celled organisms

like amoebae.

 Virology: the study of viruses.

By Type of Research

Pure microbiology research includes:

 Astro microbiology: the study of the origin of life on Earth,

and the search for extraterrestrial life.

 Evolutionary microbiology: the evolution of microorganisms.

 Cellular microbiology: the study of the structure and function

of microbial cells.

 Microbial ecology

 Microbial genetics

 Microbial physiology

 Systems microbiology: mathematical/computational modeling

of the activities of microbiological systems.

While applied microbiology research includes:

  Agricultural microbiology: the study of microorganisms that
interact with plants and soils.

 Food microbiology: the study of microorganisms that spoil

food or cause food borne illnesses. Can also study how
microorganisms are used in food production, such
as fermentation of beer.

 Medical microbiology: the study of microorganisms responsible

for human disease.

 Microbial biotechnology: using microbes in industrial

or consumer products.

 Pharmaceutical microbiology: the study of microorganisms

used in pharmaceutical products, such as vaccines and
antibiotics.

Microbiology Careers

Most jobs in microbiology require at least a bachelor’s degree. An

individual who is interested in microbiology may obtain a bachelor’s
degree in biology or microbiology. The courseload is very similar for
each of these majors; while a microbiology major may be more
specific to the interests of someone who wants to study
microbiology, it is also possible to achieve a similar level of
specificity in the biology major by taking upper-level microbiology
courses. The biology major may be preferred if one has interests in
other subfields of biology, or if he or she is double majoring in
biology and in another field. In both the microbiology and biology
majors, students must take numerous biology courses and
laboratories, and usually they must also take courses in chemistry
(including organic), physics, mathematics, and statistics.
With a bachelor’s degree, one can become employed as a research
technician in an academic or industry laboratory and provide
technical support. One could also become a quality assurance
technician in the food, environmental, pharmaceutical, or
biotechnology industries, or with some additional training, become
a medical technologist. However, many individuals with bachelor’s
degrees in microbiology or biology go on to do further schooling.
With a master’s degree in microbiology, an individual may go on to
become a laboratory manager/coordinator or a biosafety officer.
Further schooling leading to a PhD opens up opportunities in
teaching and doing research at a university. Being a professor
requires a PhD. Most heads of research laboratories in industry have
PhDs as well. Other high-level careers involving microbiology include
becoming a consultant/adviser, administrator, or lab director.

THEORY OF SPONTANEOUS GENERATION

Spontaneous Generation Definition

Spontaneous generation is an incorrect and obsolete hypothesis

about the possibility of life forms being able to emerge from non-
living things.

Spontaneous Generation Theory

The theory of spontaneous generation, first comprehensively posited

by Aristotle in his book ”On the Generation of Animals” around
350 B.C., aims to explain the seemingly sudden emergence of
organisms such as rats, flies and maggots within rotting meat and
other decomposable items. The theory suggests that organisms do
not descend from other organisms or from a parent, and only
require that certain conditions in their environment be fulfilled in
order for creation to occur.

Aristotle theorized that non-living matter contained a “vital heat”

called pneuma—the concept of a “breath of life” and translated
later as “anima” meaning “soul” in Latin—and a combination of
the four elements believed to make up all life: earth, air, fire and
water.

He suggested that animals and plants could arise from earth and
liquid, because there was “vital heat” within all air, there is air in
water, and there is water in earth, meaning there is “vital heat” or
“soul” within everything.

His explanation of the spontaneous generation was as follows:

“… LIVING THINGS FORM QUICKLY WHENEVER THIS AIR AND

VITAL HEAT ARE ENCLOSED IN ANYTHING. WHEN THEY ARE SO
ENCLOSED, THE CORPOREAL LIQUIDS BEING HEATED, THERE
ARISES AS IT WERE A FROTHY BUBBLE. WHETHER WHAT IS
FORMING IS TO BE MORE OR LESS HONORABLE IN KIND
DEPENDS ON THE EMBRACING OF THE PSYCHICAL PRINCIPLE;
THIS AGAIN DEPENDS ON THE MEDIUM IN WHICH THE
GENERATION TAKES PLACE AND THE MATERIAL WHICH IS
INCLUDED.”

Examples of Spontaneous Generation

Bougonia

One of the first accounts relating to spontaneous generation was by

the Roman poet Virgil. He described, as a recipe, the process in
which one could make synthetic bees.

The readers were instructed to beat a bovine calf to death, block up

its mouth and nose, before leaving the carcass on a bed of
cinnamon sticks and thyme.

He noted that creatures would magically appear “first voide of

limbs, but soon awhir with wings”—presumably this is referring to
maggots, which subsequently develop in to bees.

Virgil called the process described in the recipe “Bougonia”.

Spontaneous Generation of Mice

The “recipe” for making a mouse requires that sweaty underwear

should be placed over an open-mouth jar containing husks of wheat
inside for around 21 days.

A simple explanation: mice like to eat wheat and, with ease of

entering a jar and finding a dark and safe space, would most likely
to find themselves at home and have a few offspring in the new
nest.

Scorpions

The European chemist Jean Baptiste van Helmont stated that

scorpions could be manufactured by carving an indentation in to a
brick, filling the hole with basil and covering the arrangement with
another brick.

After leaving it in the sun for a couple of days, one could return to
the brick formation and would be amazed to find that

“FUMES FROM THE BASIL, ACTING AS A LEAVENING AGENT,

WILL HAVE TRANSFORMED THE VEGETABLE MATTER INTO
VERITABLE SCORPIONS”!

Other Examples

 Wet soil after a flood was believed to create amphibians such

as frogs and toads.

 Garbage in the streets was thought to create rats.

 Salamanders were thought to be borne within fire (they often

hide inside logs and were probably trying to escape the blaze!).

 Oyster shells were believed to form as the earth solidified

around them and the “vital heat” grew the creature within.

 Crocodiles in Egypt were thought to have emerged from the

mud with the sunshine as a catalyst.

The Disproving of Spontaneous Generation Theory

Francesco Redi, 1626-1697

Francesco Redi was an Italian physician and the first scientist to

suspect that the theory of spontaneous generation may be flawed,
so he set up a simple experiment. He placed fresh meat into two
different jars, one with a muslin cloth over the top, and the other
left open. A few days later, the open jar contained maggots, while
the covered container did not. He saw this as proof that maggots
had to come from fly eggs and could not spontaneously generate.

John Needham, 1731-1781

Over 100 years later, John Needham, an English naturalist and an

avid supporter of spontaneous generation theory, performed an
experiment in which he boiled up a broth and poured it into a
covered flask—at this time, people were aware that the process of
boiling removed the microorganisms that they called “animacules”.
After a short while, the broth was filled with microorganisms, a
revelation to Needham who claimed these had arisen through
spontaneous generation. His experiment was contested for the fact
he did not heat the broth for long enough and his animacules were
heat resistant.

Lazzaro Spallanzani, 1729-1799

Another Italian scientist, Lazzaro Spallanzani, performed a similar

experiment to Needham and found that if the broth was heated
after the flask was sealed rather than before, the organisms did not
generate. He decided that Needham’s broths had been
contaminated between the boiling pan and the flask.

Needham’s response claimed that air was necessary for spontaneous

generation and that the “vital heat” in the air had been destroyed
during Spallanzani’s experiment.
Louis Pasteur, 1822 – 1895

Finally in 1859, a French scientist named Louis Pasteur designed a

series of flasks with the necks bent into an S shape. The necks were
fashioned so that fresh air could reach the flasks, but were bent in
such a way that any air-borne microbes would be trapped at the
bottom of the curves.

He boiled the broth inside the flask and did not see any microbes in
the broth for many months. When he eventually removed the top
from the flask and left it off, he found the liquid to be teaming
with microorganisms within a few days. Therefore, he had proved
that the microbes from which life arises are present within the air
and are not spontaneously
generated!

The image shows a simple

diagram of Pasteur’s experiment.

Contributions of Leeuwenhoek
CONTRIBUTIONS OF LOUIS PASTEUR

Louis Pasteur and his contributions

 Louis Pasteur was a French chemist and microbiologist
considered the most important founders of Microbiology.
 Microbiology developed as a scientific discipline from the era of
Louis Pasteur (1822- 1895) himself.
 He first coined the term “microbiology” for the study of
organisms of microscopic size. For his innumerable contributions
in the field, he is also known as the Father of Microbiology.
 He is renowned for his discoveries of the principles
of vaccination, microbial fermentation and pasteurization.
 He is remembered for his remarkable breakthroughs in the
causes and prevention of diseases.
 He is regarded as one of the three main founders
of bacteriology, together with Ferdinand Cohn and Robert Koch.
 Pasteur’s academic positions were numerous, and his scientific
accomplishments earned him France’s highest decoration,
the Legion of Honor, as well as election to the Académie des
Sciences and many other distinctions.
 Today there are some 30 institutes and an impressive number
of hospitals, schools, buildings, and streets that bear his name-
a set of honors bestowed on few scientists.

Major Contributions of Pasteur

The studies on fermentation led Pasteur to take interest to work in

microbiology. His contributions to microbiology are as follows:
 He disproved the theory of spontaneous generation of disease
and postulated the germ theory of disease: He stated that
disease cannot be caused by bad air or vapor but it is produced
by the microorganisms present in air.
 The doctrine of spontaneous generation was disapproved by his
experiments that showed that without contamination,
microorganisms could not develop.
 He proposed the principles of fermentation for preservation of
food.
 He introduced the sterilization techniques and developed steam
sterilizer, hot air oven and autoclave.
 He described the method of pasteurization of milk and wine.
 He reduced mortality from puerperal fever. He had also
contributed for the vaccine development against several
diseases, such as anthrax, fowl cholera and rabies.
 Liquid media concept: He used nutrient broth to grow
microorganisms.
 He was the founder of the Pasteur Institute, Paris.
Besides in microbiology, Pasteur made significant discoveries in
chemistry, most notably on the molecular basis for
the asymmetry of certain crystals and racemization.
 Early in his career, his investigation of tartaric acid resulted in
the first resolution of what is now called optical isomers.
 His work led the way to the current understanding of a
fundamental principle in the structure of organic compounds.

Pasteur’s experiment of the Swan Neck Flask

Figure: Louis Pasteur’s spontaneous generation experiment
illustrates the fact that the spoilage of liquid was caused by
particles in the air rather than the air itself. These experiments
were important pieces of evidence supporting the idea of germ
theory of disease.
 Pasteur first filtered air through cotton and found that objects
resembling plant spores had been trapped. If a piece of cotton
was placed in a sterile medium after air had been filtered
through it, microbial growth appeared.
 Next he placed nutrient solutions in flasks, heated their necks in
a flame, and drew them out into a variety of curves, while
keeping the ends of the necks open to the atmosphere. These
flasks looked like the neck of swans hence giving the famous
experiment its name.
 Pasteur then boiled the solutions for a few minutes and allowed
them to cool.
 No growth took place even though the contents of the flasks
were exposed to the air.
 Pasteur pointed out that no growth occurred because dust and
germs had been trapped on the walls of the curved necks.
 If the necks were broken, growth commenced immediately.
 By this Pasteur proved that all life even microbes arose only
from their like and not de novo (germ theory of disease).
Pasteur had not only resolved the controversy of origin of
microorganisms but also had shown how to keep solutions sterile
with this one single experiment.

CONTRIBUTIONS OF ROBERT KOCH

Robert Koch

Robert Koch, in full Robert Heinrich Hermann Koch, (born Dec. 11,
1843, Clausthal, Hannover [now Clausthal-Zellerfeld, Ger.]—died
May 27, 1910, Baden-Baden, Ger.), German physician and one of
the founders of bacteriology. He discovered
the anthrax disease cycle (1876) and the bacteria responsible
for tuberculosis (1882) and cholera (1883). For his discoveries in
regard to tuberculosis, he received the Nobel Prize for Physiology or
Medicine in 1905.

Robert Koch and Koch’s Postulates

 Heinrich Hermann Robert Koch (1843 – 1910) provided

remarkable contributions to the field of microbiology. He was a
German general practitioner and a famous microbiologist.
 He is credited to be one of the founders of the specific field of
modern bacteriology.
 As the founder, he identified the specific causative agents of
tuberculosis, cholera, and anthrax and gave experimental
support for the concept of infectious disease, which included
experiments on humans and animals.
 For this he is also regarded as a pioneer of public health, aiding
legislation and changing prevailing attitudes about hygiene to
prevent the spread of various infectious diseases.
 For his work on tuberculosis, he was awarded the Nobel Prize in
1905 in Physiology or Medicine.

Major Contributions of Koch’s

 He investigated the anthrax disease cycle in 1876, and studied

the bacteria that cause tuberculosis in 1882 and cholera in
1883.
 He discovered bacteria such as the anthrax bacilli, tubercle
bacilli and cholera bacilli.
 Koch observed the phenomenon of acquired immunity.
 He introduced solid media for culture of bacteria. Koch
pioneered the use of agar as a base for culture media. He
developed the pour plate method and was the first to use solid
culture media for culture of bacteria.
 Koch also developed media suitable for growing bacteria isolated
from the body. Because of their similarity to body fluids, meat
extracts and protein digests were used as nutrient sources. The
result was the development of nutrient broth and nutrient agar
media that are still in wide use today.
 He also introduced methods for isolation of bacteria in pure
culture.
 He described hanging drop method for testing motility.
 He introduced staining techniques by using aniline dye.
 He invented the hot air oven and steam sterilizer, and also
introduced methods to find out the efficacy of antiseptics.
 Koch’s Phenomenon: Robert Koch observed that guinea pigs
already infected with tubercle bacilli developed a
hypersensitivity reaction when injected with tubercle bacilli or
its protein. Since then, this observation was called as Koch’s
phenomenon.
 The medical applications of biotechnology still heavily depend on
the Koch’s principles of affirming the causes of infectious
diseases.
 Contributions of Germ Theory

 Building on the early work of Louis Pasteur and the germ

theory of disease, Robert Koch established the basic scientific
requirements used to demonstrate that each specific disease is
caused by a specific microorganism.
 The first direct demonstration of the role of bacteria in causing
disease came from the study of anthrax by the German
physician.
 These requirements were based on Koch’s experiments with
anthrax isolated from diseased hosts, and are known as “Koch’s
Postulates”.

The Experiment

In the experiment, Koch injected healthy mice with a material from

diseased animals, and the mice became ill. After transferring
anthrax by inoculation through a series of 20 mice, he incubated a
piece of spleen containing the anthrax bacillus in beef serum. The
bacilli grew, reproduced, and produced spores. When the isolated
bacilli or spores were injected into mice, anthrax developed.
During Koch’s studies on bacterial diseases, it became necessary to
isolate suspected bacterial pathogens. His criteria for proving the
causal relationship between a microorganism and a specific disease
are known as Koch’s postulates.

Koch’s Postulates

Koch’s Postulates consist of the following four rules:

 1. The microorganism must be identified in all individuals affected
by the disease, but not in healthy individuals.
2. The microorganism can be isolated from the diseased individual
and grown in culture.
3. When introduced into a healthy individual, the cultured
microorganism should cause disease.
4. The microorganism must then be re-isolated from the
experimental host, and found to be identical to the original
microorganism.

Limitations of Koch’s Postulates

While Koch’s Postulates were developed as general guidelines for the

identification of infectious causes of disease, there are some inherent
limitations that could not be resolved at the time.
 Viruses were not yet able to be cultured during the 1800’s.
Thus, while it appeared that an infectious agent was responsible
for certain diseases, the lack of available techniques to isolate
and culture viruses meant that not all Koch’s Postulates could
be met.
 The third postulate stipulates that the experimental host
“should” exhibit disease, not “must”. This is because
asymptomatic carriers, immunity, and genetic resistance are
possible.
 Koch’s Postulates do not account for prion diseases and other
agents that cannot be grown in culture.
 Most of the human bacterial pathogens satisfy Koch’s postulates
except for those of Mycobacterium leprae and Treponema
pallidum, the causative agent of leprosy and syphilis,
 respectively. Both these bacteria are yet to be grown in cell-free
culture media.
Therefore, Koch’s Postulates have subsequently been revised to
account for recent molecular advances and are no longer an
absolute requirement of infectious causality.
CHARACTERISTICS OF BACTERIA

Bacteria Definition

Bacteria are single-celled microorganisms with prokaryotic cells,

which are single cells that do not have organelles or a true nucleus
and are less complex than eukaryotic cells. Bacteria with a capital B
refers to the domain Bacteria, one of the three domains of life. The
other two domains of life are Archaea, members of which are also
single-celled organisms with prokaryotic cells, and Eukaryota.
Bacteria are extremely numerous, and the total biomass of bacteria
on Earth is more than all plants and animals combined.

Evolution of Bacteria

Bacteria first arose on Earth approximately 4 billion years ago, and

they were the first forms of life on Earth. For 3 billion years,
bacteria and archaea were the most prevalent kinds of organisms
on Earth. Multicellular eukaryotes did not appear until around 1.6-
2 billion years ago. Eukaryotic cells, which make up all
protists, fungi, animals, and plants, also contain what was once
bacteria; it is thought that the mitochondria in eukaryotes, which
produce energy through cellular respiration, and chloroplasts in
plants and algae, which produce energy through photosynthesis,
both evolved from bacteria that got taken up into cells in an
endosymbiotic (mutually benefiting) relationship that became
permanent over time.

Bacteria Characteristics

Bacteria are single-celled organisms. They lack organelles such as

chloroplasts and mitochondria, and they do not have the true
nucleus found in eukaryotic cells. Instead, their DNA, a double
strand that is continuous and circular, is located in a nucleoid. The
nucleoid is an irregularly shaped region that does not have
a nuclear membrane. Bacteria also have a cell membrane and a cell
wall that is often made of peptidoglycan. Together,
the cell membrane and cell wall are referred to as the cell envelope.
Many bacteria need a cell wall in order to survive.

Reproduction occurs through binary fission, which is the splitting of

a bacterial cell after it reaches a certain size. Bacteria reproduce
asexually, so the two daughter cells that result from binary fission
have the same DNA as the parent cell. However, some bacteria can
also exchange genetic material among one another in a process
known as horizontal gene transfer. This method involves two
already existing bacteria; it is not a form of transmission from
parent to child.

Bacteria Shapes

Bacteria come in a myriad of shapes. The three main shapes of

bacteria are coccus, spiral, and bacillus.
  Cocci are bacteria that are spherical or ovoid in shape. Some
cocci remain attached after binary fission, even though
separate cells have been formed. For example, diplococci are
cocci in pairs, streptococci are chains, and staphylococci are
clusters of multiple cocci. Tetrads are square arrangements of
four cocci, while sarcinae are cubes of eight cocci.

 Spiral bacteria are, as the name suggests, spiral-shaped.

Spirillums are thick, tough spirals. Spirochetes are spirals that
are thin and flexible. Vibrios are comma-shaped rods with a
small twist.

 Bacilli are rod-shaped bacteria. Like cocci, bacilli can be

solitary or arranged together. Diplobacilli are two bacilli
arranged next to each other, and streptobacilli are chains of
bacilli.

Bacteria can also be other shapes such as filamentous (long and

thin), square, star-shaped, and stalked. This diagram depicts the
numerous shapes of bacteria.
Types of Bacteria

The cell wall also makes Gram staining possible. Gram staining is a
method of staining bacteria involving crystal violet dye, iodine, and
the counterstain safranin. Many bacteria can be classified into one
of two types: gram-positive, which show the stain and appear
violet in color under a microscope, and gram-negative, which only
show the counterstain, and appear red. Gram-positive bacteria
appear violet because they have thick cell walls that trap the crystal
violet-iodine complex. The thin cell walls of gram-negative bacteria
cannot hold the violet-iodine complex, but they can hold safranin.
This makes gram-negative bacteria appear red under Gram
staining. Gram staining is used for general identification of bacteria
or to detect the presence of certain bacteria; it cannot be used to
identify bacteria in any specific way, such as at a species level.
Examples of gram-positive bacteria include the genera Listeria,
Streptococcus, and Bacillus , while gram-negative bacteria include
Proteobacteria, green sulfur bacteria, and cyanobacteria.

Examples of Bacteria

Escherichia coli is one example of a common species of bacteria. It is

bacillus-shaped and found naturally in the intestines of many
animals including humans, where it produces vitamin K and b-
complex vitamins. E. coli is also often used in laboratory research
since it reproduces quickly and is hardy. Most strains of E. coli are
harmless to humans, but some can cause infection. E. coli infection
can result in gastrointestinal problems like diarrhea, and in more
severe cases, bacterial meningitis or pneumonia can occur.

Lactobacillus acidophilus is another bacillus-shaped species of

bacteria naturally found in places like the intestines and vagina,
where it protects against harmful bacteria. It is a probiotic, a
bacterium found in certain foods like yogurt and other fermented
foods that is consumed in order to help absorb nutrients and
replenish the body’s supply of “good” bacteria. It can also be
consumed in small amounts by people with lactose intolerance in
order to help them consume lactose.

Some bacteria can be extremely harmful, such as Clostridium

botulinum, the bacteria that causes botulism. C. botulinum produces
the neurotoxin botulinum, which is responsible for the symptoms of
botulism. Symptoms include blurred vision, nausea, trouble
breathing, muscle weakness, and paralysis. Botulinum toxin is the
deadliest known toxin; just one kilogram of botulinum would be
deadly enough to kill the entire human population.

CHARACTERISTICS OF VIRUS

Virus Definition

A virus is a chain of nucleic acids (DNA or RNA) which lives in

a host cell, uses parts of the cellular machinery to reproduce, and
releases the replicated nucleic acid chains to infect more cells. A
virus is often housed in a protein coat or protein envelope, a
protective covering which allows the virus to survive between hosts.

Virus Structure

A virus can take on a variety of different structures. The smallest

virus is only 17 nanometers, barely longer than an average sized
protein. The largest virus is nearly a thousand times that size, at
1,500 nanometers. This is really small. A human hair is
approximately 20,000 nanometers across. This means that most
virus particles are well beyond the capability of a normal light
microscope.

Here, you can only see the protein coat of the Ebola virus. Each

virus looks like a little bent worm. However, these are not cells.

Inside of the protein coat is a carefully folded RNA molecule, which

contains the information necessary to replicate the protein coat,

the RNA molecule, and the components necessary to hijack a cell’s

natural processes to complete these tasks.

The exact structure of a virus is dependent upon

which species serves as its host. A virus which replicates in
mammalian cells will have a protein coat which enables it to attach
to and infiltrate mammalian cells. The shape, structure, and
function of these proteins changes depending on the species of virus.
A typical virus can be seen below.

Viral Tegument

The above virus shows the typical structure a virus takes, a viral
genome surrounded by a shield of proteins. The various envelope
proteins will enable the virus to interact with the host cell it finds.
Part of the protein coat will then open, puncture through the cell
membrane, and deposit the viral genome within the cell. The
protein coat can then be discarded, as the viral genome will now
replicate within the host cell. The replicated virus molecules will be
packaged within their own protein coats, and be released into the
environment to find another host. While many virus particles take a
simple shape like the one above, some are much more complicated.

Phage

The above image

shows a phage, a
type of virus which
specializes on
bacterial cells. The
protein coat of a
phage is much more complex, and has a variety of specialized parts.
The head portion contains the viral genome. The collar, sheath, base
plate, and tail fibers are part of an intricate system to attach to
and inject the genome into a bacterial cell. The tail fibers grasp the
bacterial cell, pulling the base plate up to the cell wall or
membrane. The sheath and collar compress, puncture the cell, and
deposit the DNA into the bacterial cell.

Some virus molecules have no protein coat whatsoever, or have

never been identified making on. In some plant virus species, the
virus is passed from cell to cell within the plant. When seeds are
created within the plant, the virus spreads to the seeds. In this way
the virus can live within cells its entire existence, and never need a
protein coat to protect it in the environment. Other virus molecules
have even larger and more complex protein coats, and specialize on
various hosts.

Virus Classification

Scientists classify viruses based on how they replicate their genome.

Some virus genomes are made of RNA, others are made of DNA.
Some viruses use a single strand, others use a double strand. The
complexities involved in replicating and packaging these different
molecules places viruses into seven different categories.

Class I virus genomes are made of double stranded DNA, the same
as the human genome. This makes it easy for these virus molecules
to use the cell’s natural machinery to produce proteins from the
virus DNA. However, in order for DNA polymerase (the molecule
which copies DNA) to be active the cell must be dividing. Some
Class I virus molecules include sections of DNA which make the cell
actively start dividing. These virus molecules can lead to
cancer. Human papilloma virus is a sexually-transmitted Class I
virus, and can cause cervical cancer.

A Class II virus contains only a single strand of DNA. Before it can

be read by the host’s DNA polymerase enzymes, it must be
converted to double stranded DNA. It does this by hijacking the
host cell’s histones (DNA proteins) and DNA polymerase. Instead of
waiting for the cell to divide or forcing it to, Class II virus DNA
contains coding for a protein called Rep. This replication enzyme
replicates the original single-stranded virus genome. Other proteins
are created from the DNA and used to create protein coats with
the cellular machinery. The single-stranded DNA is then packaged
into these protein coats, and new virus packages are created.

Class III virus genomes are created from double-stranded RNA.

While this is unusual, these virus packages come with their own
protein, RNA polymerase. This protein can create messenger
RNA (mRNA) from the double-stranded virus RNA. The virus RNA
therefore stays within the virus capsule, and only the mRNA enters
the cytoplasm of the host. Here, the mRNA is converted into
proteins, some of which include more RNA polymerase. This RNA
polymerase creates a new double-stranded RNA, which is
encapsulated by the proteins and released from the cell.

Class IV viruses are single-stranded RNA, almost identical to mRNA

produced by the host cell. With these viruses the entire protein coat
is engulfed by an uninfected host cell. The small RNA genome
escapes the protein coat, and makes its way into the cytoplasm.
This one mRNA-like strand codes for a large polyprotein, which will
be created by the hosts ribosomes. The polyprotein naturally breaks
into different parts. Some create protein coats, while others read
and replicate the original strand of viral RNA. The virus continues
to replicate and create new, fully packed virus particles. When the
cell is completely full, it ruptures and releases the virus particles
into the blood or environment. Up to 10,000 virus particles can be
release from a single cell.

The virus genomes in Class V are also single-stranded RNA.

However, they run in the opposite direction from normal mRNA.
Therefore, the cell’s machinery cannot read them directly. These
virus molecules contain a RNA polymerase molecule which can read
in reverse. These virus molecules have large capsules, surrounded by
cell membrane and proteins. When the virus approaches a cell, its
membrane proteins bind with the cell, and it is drawn into the
cytoplasm. Here, it breaks apart, releasing the backwards viral RNA
and associated proteins. These small complexes produce regular
mRNA, which creates new virus complexes. These unfinished
complexes move to the cell surface, where they line the cell
membrane with proteins they create. When they are finished, they
wrap themselves in this membrane, and tear away from the cell.

Class VI virus genomes are the same as Class V, but they use a
different method to replicate. Class VI virus particles are known
as retroviruses. Instead of creating mRNA from the viral RNA,
these virus molecules work with a different protein. Known
as reverse transcriptase, this enzyme is able to create DNA from
the virus RNA. In doing so, the viral RNA is converted to double-
stranded DNA. This DNA then produces new virus. The DNA can
incorporate with the host DNA, and in doing so
become endogenized. This means that the DNA will remain in the
cell as long as the cell lives. If the cell is found in a germ line, such
as a sperm or egg, the virus will permanently become a part of the
host’s genome. It is estimated that 5-8% of the human genome is
left over retrovirus DNA.

The final class, Class VII, includes the pararetroviruses. Similar to

Class VI, these virus genomes use reverse transcriptase. However,
these virus genomes are package as DNA, not RNA. These viruses
insert themselves directly into the host genome, which begins
transposing the viral DNA into RNA. Most of this RNA will be
mRNA, used to create a polyprotein. Part of the polyprotein is
reverse transcriptase. This reverse transcriptase works on pieces of
RNA known as pregenome. It reads these RNA molecules and
produces the original virus DNA. This is then packaged into viral
protein coats. Class VII viruses are often found in plants, and can
travel between cells using the plasmodesmata, or they can be
carried by herbivorous insects feeding on the plants. Aphids carry
many plant diseases, as their proboscis pierces plant cell walls and
they drink the cytoplasm.

Examples of a Virus

Polio Virus

The Polio virus, which crippled President Franklin Roosevelt, is a

Class III virus. This double-stranded RNA virus encodes for 12
proteins. Like other Class III virus genomes, it reproduces by
releasing mRNA strands into the cytosol of host cells, which code
for new virus molecules. Interestingly, the polio virus was not
deadly, until people started treating their water. Before chlorinated
water, polio survived in most water sources. Thus, most infants
were exposed to polio right off the bat.

In infants, there are usually no symptoms of polio, and the immune

system responds to the virus. However, after chlorinated water was
established, most children did not experience polio. However, the
disease was not eradicated. Many people were exposed in adulthood
to pockets of polio which still persisted. These people suffered
greatly from the disease, as the immune system did not react
quickly enough to it. Like FDR, they were usually permanently
crippled from the effects of the virus on bone health. Luckily the
vaccine for polio, one of the first ever created, is easily made from
killing live polio virus with heat. The dead protein coats allow the
body to develop an immunity to the virus, without cells being
infected.

Rabies Virus

The rabies virus is a Class V virus, with a bullet-shaped protein

coat. This virus is made of linear, single-stranded RNA. The rabies
virus genome codes for five proteins, from 12,000 nucleotides.
Interestingly, the symptoms of rabies in many animals include
increased aggression. This trait, caused by where the virus attacks
and the damage it does, causes animals to bite other animals more
often than they normally would. The assembled rabies virus
particles accumulate in the saliva. Thus, when an infected animal
bites another one the virus is passed to the new animal.

Rabies virus is almost always fatal in humans, if not treated

immediately. Yearly, there are nearly 15 million post-exposure
vaccinations given for rabies. The vaccine essentially loads the body
with the dead virus, allowing a large immune response against the
virus. This can stop the virus before it gets established in the
system. If this happens, there is little chance of recovery. Dogs are
commonly vaccinated pre-exposure, which provides a general
protection to their owners on the chance they are bitten by an
animal infected with the virus.

CHARACTERISTICS OF FUNGAI
Fungi Definition

Fungi (singular: fungus) are a kingdom of

usually multicellular eukaryotic organisms that are heterotrophs
(cannot make their own food) and have important roles in nutrient
cycling in an ecosystem. Fungi reproduce both sexually and
asexually, and they also have symbiotic associations with plants
and bacteria. However, they are also responsible for some diseases
in plants and animals. The study of fungi is known as mycology.

Fungi Characteristics

Some fungi are single-celled, while others are multicellular. Single-

celled fungi are called yeast. Some fungi alternate between single-
celled yeast and multicellular forms depending on what stage of the
life cycle they are in. Fungi cells have a nucleus and organelles,
like plant and animal cells do. The cell walls of fungi contain chitin,
which is a hard substance also found in the exoskeletons of insects
and arthropods such as crustaceans. They do not contain cellulose,
which commonly makes up plant cell walls.

Multicellular fungi have many hyphae (singular: hypha), which are

branching filaments. Hyphae have a tubular shape and are split into
cell-like compartments by walls that are known as septa. These
cells can have more than one nucleus, and nuclei and other
organelles can move in between them. (There is some debate over
whether multicellular fungi are truly multicellular, because
organelles and cytoplasm can move from one cell to the other in a
process called cytoplasmic streaming. They are commonly known as
multicellular, but they are not multicellular in the same way as
plants and animals, which have enclosed cells.) A fungus’s network
of hyphae is called a mycelium.

Fungi are heterotrophs; they cannot make their own food and must
obtain nutrients from organic material. To do so, they use their
hyphae, which elongate and branch off rapidly, allowing the
mycelium of the fungus to quickly increase in size. Some fungi
hyphae even form root-like threads called rhizomorphs, which help
tether the fungus to the substrate that it grows on while allowing it
to quickly obtain more nutrients from other sources. Fungi are
opportunists, which means that they can obtain nutrients from a
wide variety of sources and thrive in a wide range of environmental
conditions. Some fungi obtain nutrients from dead organic matter;
these fungi are called saprobes and are decomposers, which break
down and get rid of dead organisms. Other fungi parasitize plants
and are responsible for plant diseases like Dutch elm disease.
However, fungi can also have symbiotic (mutually beneficial)
relationships with photosynthetic algae or bacteria, and with plant
roots. A symbiotic association of a fungus and an animal that
photosynthesizes is called a lichen, while a plant root-and-fungus
association is called a mycorrhiza.

Fungi Reproduction

Most fungi can reproduce through both sexual and asexual

reproduction. Asexual reproduction occurs through the release of
spores or through mycelial fragmentation, which is when the
mycelium separates into multiple pieces that grow separately.
In sexual reproduction, separate individuals fuse their hyphae
together. The exact life cycle depends on the species, but generally
multicellular fungi have a haploid stage (where they have one set of
chromosomes), a diploid stage, and a dikaryotic stage where they
have two sets of chromosomes but the sets remain separate.

All fungi reproduce using spores. Spores are microscopic cells or

groups of cells that disperse from their parent fungus, usually
through wind or water. Spores can become dormant for a long
time until conditions are favorable for growth. This is
an adaptation for opportunism; with a sometimes unpredictable
food source availability, spores can be dormant until they are able
to colonize a new food source. Fungi produce spores through sexual
and asexual reproduction.

Types of Fungi

There are five phyla of fungi: Chytridiomycota, Zygomycota,

Glomeromycota, Ascomycota, and Basidiomycota. The following is a
brief description of each phylum.

Chytridiomycota

Chytrids, the organisms found in Chytridiomycota, are usually

aquatic and microscopic. They are usually asexual, and produce
spores that move around using flagella, small tail-like appendages.
The chytrid Batrachochytrium dendrobatidis can cause a fungal
infection in frogs by burrowing under their skin, and it has recently
devastated populations of harlequin frogs, killing off two-thirds of
them in Central and South America.
Zygomycota

Zygomycetes are mainly terrestrial and feed off of plant detritus or

decaying animal material. They also cause problems by growing on
human food sources. One example of a zygomycte is Rhizopus
stolonifer, a bread mold. The hyphae of zygomycetes are not
separated by septa, making their mycelia essentially one large cell
with many nuclei. They usually reproduce asexually, through spores.

Glomeromycota

Glomeromycetes make up half of all fungi found in soil, and they

often form mycorrhizae with plants; in fact, 80-90 percent of all
land plants develop mycorrhizae with glomeromycetes. The fungi
obtain sugars from the plant, and in return, dissolve minerals in
the soil to provide the plant with nutrients. These fungi also
reproduce asexually.

Ascomycota

Ascomycetes are often pathogens of plants and animals, including

humans, in which they are responsible for infections like
athlete’s foot, ringworm, and ergotism, which causes vomiting,
convulsions, hallucinations, and sometimes even death. However,
some ascomycetes normally are found inside humans, such
as Candida albicans, a yeast which lives in the respiratory,
gastrointestinal, and female reproductive tracts. Ascomycetes have
reproductive sacs known as asci, which produce sexual spores, but
they also reproduce asexually.
Basidiomycota

Like ascomycetes, basidiomycetes also produce sexual spores called

basidiospores in cells called basidia. Basidia are usually club-shaped,
and basidiomycetes are also known as club fungi. Most basidiocytes
reproduce sexually. Mushrooms are a common example of
basidiomycetes.

Examples of Fungi

Fungi are sometimes overlooked in biology, especially compared to

bacteria, plants and animals. This is partially because many fungi
are microscopic, and the field of mycology did not really develop
until after the invention of the microscope. However, there are
many common examples of fungi. Yeasts are one example. As
mentioned before, Candida albicans grows naturally inside the
human body, but sometimes it can grow excessively and cause a
yeast infection. Yeast infections are extremely common; 75 percent
of women will have at least one yeast infection during their
lifetime.

Fungi are also often associated with food. Mushrooms and truffles
are examples of fungi that are sometimes edible, the latter being
highly prized in haute cuisine internationally. Molds are fungi that
grow on foods over time, causing them to spoil. Food is refrigerated
in order to prevent mold growth since few molds grow at 4°C
(39°F). However, some molds are used in the process of cheese-
making. Molds are added to soft ripened cheeses like brie, washed
rind cheeses like Limburger, and blue cheeses.
CHARACTERISTICS OF PROTOZOA

Protozoa Definition

Organisms known as protozoa include a wide range of organisms,

most of which are free-living single-celled eukaryotes. Therefore,
protozoa fit into the Domain Eukarya. Although the different phyla
of the kingdom Protista are not closely related, they are
nonetheless classified together because of their large differences
from the other kingdoms of plants, animals and fungi. The name
“protozoa” has a dynamic history, at one time including only the
“animal-like” unicellular forms of life. Today, these heterotrophic
protozoa are lumped together with the autotrophic algae and other
simple forms of life into the Kingdom Protista. While all protozoa
are eukaryotes, not all reproduce with the standard model
of mitosis that is seen in higher animal cells. Many have complex
cellular division that resembles binary fission in bacteria, on a larger
scale. Some phyla in the Kingdom Protista are autotrophic cells,
containing chloroplasts which can produce sugars from sunlight.
Although only heterotrophic organisms were considered protozoa
historically, this article will present many of the phyla within
Protista that can photosynthesize sugars. Below is an image of a
ciliate protozoa.

Some Of The Characteristics are:

1. There are about 50,000 known species of Phylum Protozoa.

2. Protozoans exhibit mainly two forms of life; free-living (aquatic,
freshwater, seawater) and parasitic (ectoparasites or
endoparasites). They are also commensal in habitat.
3. They are small, usually microscopic, not visualize without
a microscope.
4. They are the simplest and primitive of all animals.
5. They have a simple body organization. i.e. with a protoplasmic
grade of organization.
6. The body is unicellular (without tissue and organs).
7. They have one or more nuclei which are monomorphic or
dimorphic.
8. Body naked or bounded by a pellicle, but in some forms may be
covered with shells and often provided with an internal
skeleton.
9. They are solitary (existing alone/single) or colonial (individuals
are alike and independent).
10. Body shape variables may be spherical, oval, elongated or
flattened.
11. Body symmetry either none or bilateral or radial or spherical.
12. Body form usually constant, varied in some, while changing
with environment or age in many.
13. Body protoplasm is differentiated into an outer ectoplasm and
inner endoplasm.
14. The single-cell body performs all the essential and vital
activities, which characterize the animal body; hence
only subcellular physiological division of labor.
15. Locomotory organs are fingers like pseudopodia, whip-
like flagella, hair-like cilia or none.
16. Nutrition may be holozoic (animal-like), holophytic (plant-
like), saprozoic or parasitic.
17. Digestion occurs intracellularly which takes place inside the
food vacuoles.
18. Respiration occurs by diffusion through the general body
surface.
19. Excretion occurs through the general body surface, but in
some forms through a temporary opening in the ectoplasm or
through a permanent pore called cytopyge.
20. Contractile vacuoles perform osmoregulation in freshwater
forms and also help in removing excretory products.
21. Reproduction asexual (binary or multiple fission, budding,
sporulation) or sexual (conjugation (hologamy), game formation
(syngamy)).
22. The life cycle often complicated with alternation of asexual
and sexual phases (alternation of generation).
23. Encystment commonly occurs to resist unfavorable conditions
of food, temperature, and moisture, and also helps in dispersal.
24. The single-celled individual not differentiated into
somatoplasm and germplasm; therefore, exempt from natural
death which is the price paid for the body.
25. Protozoans exhibit mainly two forms of life; free-
living (aquatic, freshwater, seawater)
and parasitic (ectoparasites or endoparasites). They are
also commensal in habitat.
26. Examples: Euglena, Amoeba, Plasmodium, Paramecium,
Podophyra, etc.

CHARACTERISTICS OF ALAGE

Algae Definition
Algae is a term used to describe a large, diverse group
of eukaryotic, photosynthetic organisms. Algae can be unicellular,
live in colonies, or even be multicellular. The wide variety algae
makes them hard to classify. Algae span both terrestrial and
marine environments, growing almost anywhere there is water and
sunlight. Algae, like plants, are photosynthetic organisms. One
group of algae, the green algae, is even classified with the plants
because of how similar the organisms are.

Algae, as a group, produce a vast majority of the oxygen on Earth.

They exist in almost every part of the ocean receiving sunlight, in
enormous numbers. Many other species survive filtering algae out of
the water, and many more are dependent upon the oxygen they
produce. Algae require a variety of nutrients in addition to sunlight.
When conditions are perfect and no nutrients are limited, algae can
experience exponential growth. This can lead to algal blooms, in
which massive amounts of algae bloom at the same time. The algae
rapidly become too thick, killing many of the algae in the middle of
the bloom. Bacteria and other organisms move in to feed on the
dead algae, depleting the water of oxygen. This creates an oxygen
“dead zone” in the ocean, which can be deadly to many species.
Further, the toxins produced by some algae can be harmful or
deadly to wildlife and humans.

Algae Form and Structure

The “typical” (if there is one) algae consists of a eukaryotic cell,

resembling that of a plant, with a membrane
bound nucleus, chloroplasts, and mitochondria. The chloroplasts
photosynthesize sugars, which are broken down by the
mitochondria. While many algae species are found as free-living
unicellular organism, others take the form of colonies or
multicellular organism. Below is a Euglena, a free-living unicellular
algae. This algae has a thick pellicle, which spirals around
the cell for protection. Other algae may have cell walls, or other
protective coverings.

Other algae live in more complex arrangements. The colony of algae

below rely on each other, but still function as individuals for the
most part. As you can see, the algae on the outer edge of the
colony are specialized for defense, carrying large spines. This helps
the whole colony survive, without each algae having to produce
spikes.

The largest algae, however, exist as multicellular organisms. These

algae, like the kelp seen below, can grow hundreds of feet tall,
exploiting the entire column of light in the ocean. Unlike most
terrestrial plants, these plants are nonvascular, and do not have a
special way to transport water. Thus, they must stay in the marine
environment. They do have a number of adaptations which help
them deal with the harsh conditions of the ocean, such as floating
organs which carry them toward the light and specialized anchors
which help root them to the ocean floor.

However, there are also a class of organisms known

as cyanobacteria (blue-green algae), which photosynthesize but are
only prokaryotes. While they contain all the necessary biochemical
pathways to photosynthesize, they do not have membrane-bound
organelles or a nucleus. Thus, they are bacteria. Scientist believe
that these smallest and simplest of algae represents the chloroplast,
before the process of endosymbiosis took place. In other words,
scientists believe that cyanobacteria and chloroplasts are related,
and that chloroplasts and mitochondria are simply smaller
organisms which have coevolved with their larger cohosts

General Characteristics of Algae

Algae are eukaryotic organisms that have no roots, stems, or leaves

but do have chlorophyll and other pigments for carrying out
photosynthesis. Algae can be multicellular or unicellular.

Unicellular algae occur most frequently in water, especially in

plankton. Phytoplankton is the population of free‐floating
microorganisms composed primarily of unicellular algae. In
addition, algae may occur in moist soil or on the surface of moist
rocks and wood. Algae live with fungi in lichens.

According to the Whittaker scheme, algae are classified in seven

divisions, of which five are considered to be in the Protista kingdom
and two in the Plantae kingdom. The cell of an alga has eukaryotic
properties, and some species have flagella with the “9‐plus‐2”
pattern of microtubules. A nucleus is present, and multiple
chromosomes are observed in mitosis. The chlorophyll and other
pigments occur in chloroplasts, which contain membranes known
as thylakoids.

Most algae are photoautotrophic and carry on photosynthesis. Some

forms, however, are chemoheterotrophic and obtain energy from
chemical reactions and nutrients from preformed organic matter.
Most species are saprobes, and some are parasites.

Reproduction in algae occurs in both asexual and sexual forms.

Asexual reproduction occurs through the fragmentation of colonial
and filamentous algae or by spore formation (as in fungi). Spore
formation takes place by mitosis. Binary fission also takes place (as
in bacteria).

During sexual reproduction, algae form differentiated sex cells that

fuse to produce a diploid zygote with two sets of chromosomes. The
zygote develops into a sexual spore, which germinates when
conditions are favorable to reproduce and reform the haploid
organism having a single set of chromosomes. This pattern of
reproduction is called alternation of generations.