viruses

Chapter 2
The Microbial World
Some Basic Biological Principles
Cell Theory
Robert Hooke coined the term “cell” in 1665, based on his initial microscopic
observations of cork. These observations ultimately gave rise to the cell theory, as
postulated by Schleiden, Schwann, and Virchow, about two centuries later. The major
points of the cell theory are as follows:
1. All organisms are composed of a fundamental unit, the cell.
2. All organisms are unicellular or multicellular.
3. All cells are fundamentally alike regarding their structure and metabolism.
4. Cells only arise from preexisting cells (“life begets life”).
Life begets life is a refutation of the once popular idea of spontaneous generation, a
doctrine that proposed life could arise from non-living components (which was disproved
in the late 1800s). Viruses and prions are not composed of cells; they are acellular or
subcellular infectious agents. Neither of these two agents is considered to be alive by
most biologists.
Metabolic Diversity
Living things possess several attributes commonly associated with life, as summarized in
Table 2.1. The attributes common to life include the following: being composed of one
or more cells, requiring energy, being able to reproduce, being able to respond to stimuli,
and having the ability to grow.
Most cells obtain energy through a complex series of biochemical reactions termed
metabolism. Cells metabolize organic compounds (proteins, fats, and carbohydrates) in
food and capture the energy stored in chemical bonds by forming high-energy bonds in
adenosine triphosphate (ATP). Most microbes are heterotrophs, which require an
organic source of energy. Some microbes and plants, the autotrophs, do not need to
extract energy from organic compounds. Photosynthetic autotrophs obtain energy
directly from the sun, while chemosynthetic autotrophs obtain their energy from
inorganic compounds. Autotrophs manufacture organic compounds, and some
photosynthetic autotrophs produce oxygen (O
2
), thus, heterotrophs depend upon
autotrophs for their energy needs and as a source of carbon (Figure 2.1).
Requirement for Oxygen
Microbes have diverse requirements for O
2
. Aerobes require O
2
for metabolism, while
anaerobes do not. Many anaerobic microbes are killed by O
2
. Bacterial facultative
anaerobes actually grow better in the presence of O
2
, but they can grow in its absence.
In clinical microbiology, knowledge of the O
2
requirements of bacteria is required, as any
bacteria suspected of being anaerobes must be transported and cultured under anaerobic
conditions (Figure 2.2).
Genetic Information The genetic information of all cells is stored in molecules of
deoxyribonucleic acid (DNA). Genes are segments of the DNA molecule. Each type of
organism has its genetic characteristics encoded in DNA molecules that confer its species
identity. Thus, DNA acts as the hereditary material for cellular organisms (and DNA
viruses).
What Makes a Microbe?
Algae and some fungi are macroscopic; hence, “microscopic” is not an absolute characteristic of
microbes. Similarly, the term unicellular does not apply to those algae and fungi that are
macroscopic and clearly must be multicellular. There are even macroscopic bacteria, like the
recently discovered “monster bacteria” Epulopiscium fishelsoni and Thiomargarita namibiensis
(Box 2.1). Microbes are sometimes described as “simple” because many consist of only a single
cell or are less than a cell (viruses and prions). Consider, however, that this single cell must
fulfill all the functions of life. Hence, single-celled organisms, and even those multicellular
organisms without specialized cells, are simple only in the sense of numbers and not in a
physiological sense.
Microbe, or microorganism, is a term of convenience used to describe biological agents that are
generally too small to be seen without using a microscope. Some consider microbes to be
organisms that are at a level of organization below tissues (Figure 2.4). This organizational
hierarchy is summarized as follows: subcellular → cells → tissues → organs → organ systems.
All microbes are unicellular or multicellular, but devoid of tissues. Prions and viruses can be
properly placed at the acellular or subcellular level and are at the threshold of life.
Procaryotic and Eucaryotic Cells
Biologists divide all life into two distinct types of cells, procaryotic and eucaryotic. Procaryotes
have a simpler structure than eucaryotic cells and are primarily distinguished by lack of a true
membrane-bound nucleus. Instead, bacteria possess a DNA-rich region in the cytoplasm—the
nucleoid. Further, in procaryotic cells there are no membrane-bound organelles at all, in contrast
to the cellular anatomy of eucaryotic cells (Table 2.2 and Figure 2.5). Bacteria are procaryotic
microorganisms; protozoans, algae, fungi, and all other forms of life (except viruses and prions)
are composed of eucaryotic cells.
Microbial Evolution and Diversity
In the 1700s, the botanist Carolus Linnaeus classified all life into either the plant or the animal
kingdom. When bacteria were discovered they were placed with plants (probably because they
had a cell wall). Taxonomy, the science of classification, has become more and more complex
over the intervening years. Ernst Haeckel (1866) proposed a three- kingdom system—animals,
plants, and Protista (which included some microbes). In 1969 a five-kingdom system was
proposed by Robert Whittaker, which became accepted by most biologists. The five kingdoms
were Monera (bacteria), Protista (protozoans and unicellular algae), Fungi, Animalia, and
Plantae (Figure 2.6). In 1990 Carl Woese, along with Otto Kandler and Mark L. Wheelis,
proposed a novel classification scheme (based on rRNA analysis) that placed all life into three
”super kingdoms” or domains—Bacteria, Archaea and Eucarya (Figure 2.7). All three arose
from a single common ancestor, from which the prokaryotic Bacteria and Archaea first diverged,
followed by the eucaryotes (Eucarya). These domains all differ significantly from each other in
chemical composition and other characteristics (Table 2.3).
No matter the classification scheme, bacteria were the first forms of life on Earth. Fossilized
bacteria have been discovered in stromatolites (stratified rocks dating back 3.5 billion to 3.8
billion years, in Earth’s 4.6 billion year history). Earth’s ancient atmosphere is thought to have
been devoid of oxygen and would not have supported many familiar life forms. However, about
2 billion years ago, photosynthetic microbes evolved to use sunlight, water and carbon dioxide to
produce oxygen and carbohydrates.
Bacteria are biochemically diverse and have filled every known ecological niche. Some estimate
that fewer than 2% of bacterial species have been identified and even fewer have been cultured.
Archaea continue to be found in environments once considered too extreme or too harsh for life
at any level. Some of these bacterial “extremophiles” cannot be cultured with existing
techniques; evidence of their existence is deduced from their RNA found in environmental
samples. Hyperthermophiles (“heat lovers”), have been discovered which grow best at
temperatures above 100°C. Pyrococcus furiosus lives in boiling water bubbling from undersea
hot vents and can’t grow in temperatures below 70°C (Figure 2.8a). Other extremophiles, the
psychrophiles, may grow at temperatures below –20°C and thrive in Arctic and Antarctic
environments (Figure 2.8b). Some extreme halophiles (“salt lovers”) can only grow in high
salinity, as found in the Dead Sea (Figure 2.9). Archaea have even been found, which, as a
byproduct of their metabolism, produce methane (natural gas). Given their unusual growth
requirements, no Archaea have been found to cause disease in humans.
A comprehensive survey of microbial life on Earth is underway. Microbes were the first life
forms on this planet, and how they arose is of great interest to science. A bacterium arising from
a “primordial soup” is one common suggestion for life’s origin, and a few hypothesize that Earth
was seeded by microbes from Mars (an explanation that is intriguing, but lacks hard evidence at
this point).
Introducing the Microbes
Although there is no universally accepted definition for microbes, much is known about their
biology and biochemical composition, as summarized in Table 2.4. Acellular and unicellular
microbes extend over a range of sizes from nanometers (billionths of a meter) to micrometers
(millionths of a meter), as depicted in Figure 2.11.
Prions
Prions are infectious protein particles, and like viruses they are acellular. However,
unlike viruses, they lack nucleic acid (i.e., a DNA or RNA genome). Prions reproduce in
a unique way from a normal protein commonly found in the brain—an infectious prion
molecule physically interacts with the normal protein, converting it to the infectious
form. This cycle continues, amplifying the infectious prion particles until a neurological
disease process results in humans and other mammals (e.g., BSE or “mad cow disease”).
Viruses
Viruses are acellular infectious agents containing genomic RNA or DNA, never both.
They are obligate intracellular parasites—requiring a living cell for their own
replication. Viruses must co-op the molecular machinery of the host cell for their own
synthesis and frequently kill the cell they infect. Viruses are submicroscopic, thus
requiring an electron microscope for their visualization (Figure 2.12).
Bacteria
Bacteria are the best-known microbes (Figure 2.13). They are unicellular, procaryotic
cells; most possess a cell wall (except for the mycoplasmas). Bacteria can be seen with a
light microscope, and they replicate asexually, by binary fission. Metabolically, many
bacteria are heterotrophs (using organic compounds as an energy source). Other bacteria
are autotrophs, using the sun or inorganic molecules, as a source of energy. Because of
this metabolic flexibility, bacteria are found ubiquitously in nature. Although a few
bacterial species are pathogenic for humans, the vast majority are harmless. Moreover,
all other life depends upon bacteria for its existence.
Protozoans
Protozoans are unicellular, heterotrophic, eukaryotes, and they are traditionally classified
by their means of locomotion. Most are harmless microbes; however, some of the best-
known and most significant human diseases are caused by protozoans (e.g., malaria,
sleeping sickness, amebic dysentery, etc.).
Algae
Algae are eukaryotic autotrophs that generate oxygen during photosynthesis.
Dinoflagellates and diatoms are two types of unicellular algae (plankton), which are a
primary source of food for larger heterotrophic organisms in the world’s oceans and
lakes. Algae are important to the planet’s ecology. While none infect humans, some
marine algae (like the dinoflagellate Gymnodinium breve) produce neurotoxins that are
capable of harming marine life and any humans who consume algae-contaminated fish
and shellfish. “Red tide” is the name for a bloom of toxic marine dinoflagellates (the
dinoflagellates in a bloom grow to such high density, that they literally turn the tide red).
Fungi
Fungi are non-motile, heterotrophic eucaryotes, possessing a cell wall and may reproduce
sexually or asexually (Figure 2.16). They are commonly subdivided into the groups
yeasts or molds. Yeasts are unicellular cells, much larger than bacteria. Molds are the
more common type; they are multicellular and form a tangled mass of long, branched
filaments, termed hyphae. A mass of hyphae is visible to the unaided eye. Like other
microbes, fungi are usually harmless or even beneficial, but a relative few are pathogenic
for humans. Some fungi are opportunistic pathogens, only causing disease in those with
a depressed immune system, as in the case of AIDS.
Viruses fascinate me. How is that they are not living
organisms? Do you have an idea how did they evolve from
other organisms? I was thinking that they probably evolved
from the mitochondria, is it possible?
Answer !
Viruses are not classified as being alive because they don’t have
their own machinery for reproducing. They can only take over the
machinery of cells, turning them into virus factories. But not
everyone agrees with this system. Someone might say, “ey,
parasites need to reproduce inside other organisms, but they’re
alive.! That would be a reasonable argument for saying that viruses
are a form of life. " tell my students that people like to make nice
neat categories, but the natural world almost never fits into them.
#utting things into categories can be helpful, but we have to
remember that the categories are usually artificial and should not
get in the way of understanding all of the ama$ing diversity of the
world.
"’m really impressed that you thought about the mitochondria as a
possible ancestor for viruses. They best story we have today is that
mitochondria were once free%living bacteria. &id viruses evolve from
bacteria' (aybe. "t is difficult to say because it may have happened
) billion years ago, and &*+ ,ust doesn’t last that long. Viruses
don’t seem to fossili$e well, either. Since bacteria were around
before the cells that we call “eukaryotic! -plant, animal, fungal, and
protist cells., that may be what happened. Some scientists think that
different groups of viruses evolved independently, maybe some
even came from eukaryotic cells, and some from bacterial cells.
"f viruses are basically parasites that evolved from living bacteria,
would that be another argument for saying that they are a type of
life'
/e still know very little about viruses and bacteria, compared to
what we know about multicellular organisms. 0ou may want to
consider a career in microbiology if you want to e1plore them.
Thanks for asking,
Answer "!
Viruses fascinate me too, so " actually wrote an article all about
them. 2eel free to check it out here3
viruses origins
" think it will answer your 4uestions -and maybe raise some more5..
There6s actually a lot of debate over whether they are 7alive7 or not,
and some scientists think that we might have evolved from viruses,
or something like them5 Viruses have definitely been around for a
very long time. See the article for more details.
Answer #!
Viruses are not considered 7alive7 because they lack many of the
properties that scientists associate with living organisms. #rimarily,
they lack the ability to reproduce without the aid of a host cell, and
don6t use the typical cell% division approach to replication.
8ssentially, however, this is ,ust how scientists have defined the
word. "f viruses were classified as living, other types of self%
replicating genes, proteins, and molecules would make the list as
well.
There are a few theories on the origin of viruses. Since there is no
historical record of the earliest viruses, the only evidence available
is from current species. "ndeed, one theory suggests that viruses
may have arisen from parasitic cells which lost their cellular
structure through evolution. owever, there isn6t a lot of evidence
from current cells that shows this type of transition is possible.
+nother theory is that they evolved along with living cells, from
genes or proteins that happened to be self%replicating. "t would
seem that since the spectrum of viruses around today is so wide,
they likely evolved through many different pathways.
Answer $!
0es, viruses are interesting. Viruses don6t fit the definition of life, but
they6re certainly not dead either5 They6re an interesting e1ample of
how we can6t really separate stuff into 9 simple categories % :iving
and *on%living. Viruses seem to be in between those 9 categories.
+nd the 4uestion gets even more interesting when scientists talk
about life on other planets, because this might be very different from
life on earth. They call it 7:ife as we &on6t know it.7
Some scientists are still debating about /hat is :ife' "n fact, " wrote
a little article about it last fall, for a collection of ,ournal articles all
about that sub,ect.
" think viruses probably evolved from simple cells such as bacteria
and archaea that don6t have a nucleus. ;eep asking 4uestions5
Best wishes,
Answer %!
81cellent, viruses +<8 fascinating5 + virus particle is made up of 9
main parts3 genetic material -either <*+ or &*+. and a coat that is
made up of protein and sometimes lipids -fats. that protect the
genetic material. + virus can live outside of a host cell but it can not
reproduce without a host5
Scientists argue a lot about whether viruses are in fact living
organisms or ,ust organic structures interacting with living
organisms. Some properties of viruses make them seem alive like
the fact that they have genetic material and that they make copies
of themselves to reproduce. =n the other hand, people will argue
that viruses do not have any structure to their cells -which even
simple living organisms have., they do not have the ability to make
their own chemical products and need a host cell to do that for them
and that is why they can not reproduce without a host cell. This
debate is not going to be settled anytime soon, but you can decide
for yourself whether you think viruses are living or not5
/here viruses originated is also something that scientists disagree
about. There are ) main ideas for how viruses evolved in the first
place. >. Viruses could have started out as bacteria and ,ust lost all
the genes they needed to survive on their own. 9. Viruses could
have begun as small pieces of genetic material that escaped from a
larger organism and infected another. ). Viruses simply started out
as viruses when proteins and genetic material mi1ed and that these
particles have been living this way -infecting living cells to replicate.
for billions of years, ever since life itself began. Viruses do not form
fossils, which makes it really hard for scientists to determine where
e1actly they came from.
2or some more information on viruses, check out these two links3
virus>
virus9
Answer &!
Viruses are very strange organisms. They are not really considered
to be living creatures. This is because they are not capable of
replicating themselves on their own. Viruses need to infect another
cell in order to replicate. This is because they do not have all the
genes necessary for replication. Viruses are made up of their
genetic material and a few proteins, which is encapsulated in a
protein coat. They attach to a living cell and in,ect their nucleic acids
-and sometimes release their proteins as well. into a cell. The viral
nucleic acids then takes over the cell6s own proteins and makes the
cell replicate the viral genetic material. =nce the virus has
replicated its genome and made the proteins for its coat, it will
assemble and then cause its host cell to burst open. This releases a
new set of viruses to infect other cells. Thus, without another living
cell, viruses cannot replicate and spread.
The evolutionary origin of viruses is something that is unknown. "t is
possible that viruses were actually cellular organisms once, which
became adapted to an intracellular life style. This is similar to how
mitochondria are believed to have evolved. owever, it is unlikely
that viruses evolved directly from mitochondria. Viruses were likely
around long before mitochondria e1isted. +nother theory is that
viruses originated from genetic material that co%evolved with cellular
organisms to become separate from the cellular genome and
eventually became more comple1, resulting in the virus particles we
know today.
Answer '!
Viruses lack the cellular machinery to be able to reproduce
themselves? without using the genetic code of a cell as their host,
the genetic information contained within a virus is meaningless. +n
analogy " could make is that viruses are basically software, and
software re4uires hardware -in this case, a cell. to run on. 2or this
reason, most definitions of life do not identify viruses as living
organisms, because they aren6t actually @organisms@.
This said, viruses do possess a lot of life% like 4ualities, including the
ability to carry information, reproduce -with help., and evolve under
natural selection. Saying that viruses aren6t living in some sense is
also missing the point.
Viruses are strands of &*+ or <*+ contained within protein
sheathes and seem to be genetically related to the organisms that
they infect, as if they evolved from their hosts6 genomes. This
means that viruses probably evolved multiple times from different
ancestors. " don6t know of any viruses thought to have evolved from
mitochondria, or that can even infect mitochondria, but " see no
reason why it isn6t possible that some could have.
Alick ere to return to the search form.
http://scienceline.ucsb.edu/getkey.php?key=3316
Viruses are in the news. 0ou6ve probably heard about +vian 2lu, /est *ile Virus, "V, and S+<S.
0ou probably know about chicken po1, measles, rabies, or polio. "6m sure you6ve had a 7cold.7
0our nose is runny, you snee$e a lot and have a sore throat. 0our eyes might be red, and you
might feel sore all over and have a fever. + 7cold7 and many other diseases are caused by a
tiny, microscopic living thing called a virus. #hoto. Aourtesy of the (icrobe:ibrary.org? B Cean%0ves Sgro, Dniversity of
/isconsin.
(hat is a virus? + virus is a microbe. + microbe is a tiny one%celled living organism, too small to
be seen with ,ust your eyes. =ther types of microbes are3 bacteria, proto$oa, and
fungi. Some people call microbes 7germs7.
*ot all microbes are bad... (any bacteria live with us all the time, and help us do
ama$ing things like make yogurt, pickles, cheese, and even break down some
garbage. (icrobes are all around us. They e1ist on our skin, and on the skin of
fruit.http3EEwww.microbeworld.orgEhtmEaboutmicroEmicrobesEtypesEbacteria.htm
/hat is a germ'

ere is a photo of one
type of virus.
This photo gallery has even more images.
Discovery of the Virus How big is a virus'
How does a virus infect you? Viruses are everywhere but they need to
get inside a human, an animal or a plant to make them sick. "n fact, they
must invade a cell, called a host cell, in order to grow and reproduce. (ost
can6t survive long unless they6re in a living host. =nce inside, though, they can
spread and make other people sick. Some can live awhile on something like a desk, or doorknob
so it6s important for you to wash your hands regularly so you don6t become infected5Viruses can
enter us through the nose, mouth or breaks in the skin.
Viruses are made of a small collection of genetic material -&*+ or <*+. encased in a
protective protein coat called a capsid. Take a peek at what6s inside a virus...
"s a virus +:"V8' There is some debate about this. owever, most scientists say they are not
alive because they cannot grow or reproduce on their own.
They need a host cell to multiply.
)hen what happens?
=nce inside a host cell they follow these basic steps in order to fool the host cell into making
make copies of the virus that might then infect living organisms. This is called the lytic cycle.
)he *ytic +ycle, or how a virus fools a host cell into making more viruses
+ virus attaches to a host cell. -+ll viruses have
some type of protein on the outside coat that
7recogni$es7 the proper host cell..
The en$ymes make parts for more new virus
particles
The virus, or a virus particle, enters or releases
its genetic instructions into the host cell
The new particles assemble the parts into new
viruses.
The in,ected genetic material gives instructions
to the host cell6s en$ymes
The new virus particles leave the host cell, ready
to infect other cells
&iscover more about viruses, bacteria , proto-oa, fungi.
.our body/s Immune 0ystem to the rescue111
0our body has a defense against viruses. "t is called the Immune 0ystem. "f a virus
makes it past your tough skin, or the sticky mucus and little hairs called cilia lining
your breathing tube then this system takes over.
Here/s how it works...The immune system is an organi$ation of different types of cells, tissues
and en$ymes work together to identify and eliminate all invading substances in your body. 8ach
part of the immune system has it6s own speciali$ed ,ob.
(hite blood cells are your main defense. They patrol your body. /hen they
come across an antigen, they produce an antibody that only works to fight against
that particular antigen. Some antibodies destroy antigens while others make it easier
for white blood cells to destroy the antigen.
Trillions and trillions of white blood cells gobble the enemy. Sometimes, though, your body
needs help from the medicines doctors give you. =ne of these medicines is called a vaccine.
:earn about vaccines here.
There are hundreds of different kinds of viruses, and they’re constantly changing. 0ou
can6t catch the same virus teice. The immune system can remember the response later
if the foreign substance invades the body again, and it gets right to work
http://idahoptv.org/dialogue4kids/season8/viruses/facts.cfm
Virus
A virus is a microscopic particle that can infect the cells of a biological organism.
Viruses can only replicate themselves by infecting a host cell and therefore cannot reproduce on their
own.
At the most basic level, viruses consist of genetic material contained within a protective protein coat called
a capsid; the existence of both genetic material and protein distinguishes them from other virus-like
particles such as prions and viroids.
They infect a wide variety of organisms: both eukaryotes (animals, fungi and plants) and prokaryotes
(bacteria).
A virus that infects bacteria is known as a bacteriophage, often shortened to phage.
The study of viruses is known as virology, and those who study viruses are known as virologists.
It has been argued extensively whether viruses are living organisms.
Most virologists consider them non-living, as they do not meet all the criteria of the generally accepted
defnition of life.
They are similar to obligate intracellular parasites as they lack the means for self-reproduction outside a
host cell, but unlike parasites, viruses are generally not considered to be true living organisms.
A primary reason is that viruses do not possess a cell membrane or metabolise on their own -
characteristics of all living organisms.
Examples of common human diseases caused by viruses include the common cold, the fu, chickenpox
and cold sores.
Serious diseases such as Ebola, AIDS, bird fu and SARS are all also caused by viruses.
http://www.sciencedaily.com/articles/v/virus.htm