Why are viruses, viroids prions

virus viroid prion

not considered to be living organisms ?

I. Viruses (Latin word virus = toxin or poison)
• sub-microscopic particles [20-300 nm] - smaller than a
bacterium

SARS virus bacteriophage tobacco mosaic virus

• consist of genetic material (a nucleic acid; DNA or RNA])
contained within a protective protein coat called a capsid
.
- do not contain all 4 biomolecules
• do not have a cellular structure (= basis for ---> non-living
• unable
life) to replicate outside of a living system [do not
reproduce]
• they infect the cells of living organisms [incl. bacteria]
= “infectious agents” because they cause disease
 Viruses inject their DNA or RNA into the cells of living organisms.

Capsid is an outer protein coat consisting of repeating units of

just a few kinds of proteins.
Capsid protects the virus but also has sites on it that can bind onto
the host cell’s surface.
Some viruses also have an outer viral envelope made of glycoproteins
and lipids obtained from the membranes of their host cells.

https://www.genome.gov/genetics-glossary/Virus
Bacteriophages infect bacteria.
They keep bacterial
populations under control so
https://commons.wikimedia.org/wiki/File:Figure_21_01_03.png they don’t overrun the planet.
Is evidence that viruses can swap genes with cellular
organisms and are agents of genetic diversity.
I already discussed the role of bacteriophages transporting
from one bacterial to another in a process called
genes
transduction Some RNA viruses are retroviruses.

A retrovirus is a specific type of RNA virus that can reverse

transcribe its RNA into DNA, which is then integrated
into the host cell's genome.

These virus can persist in the host cell and be passed on

to future generations of the host cells.
endogenous retroviruses (ERVs) are remnants of once
infectious exogenous retroviruses that have become fixed in
our DNA and are now inherited in a Mendelian manner.
Genome-sequencing of many species has revealed that
ERVs have a ubiquitous presence in vertebrate genomes,
and they constitute over 8 % of the human genome.

That’s four times more of the human genome than

protein-encoding genes.

Two of the very few ERVs known to encode functional

proteins in humans, syncytin-1 and syncytin-2.

Syncytins are critical during embryogenesis, when they

contribute to the formation of a multinucleate tissue
layer in mammalian placentas which separates the maternal
and fetal bloodstreams.
Viruses

Cant reproduce themselves on their

own nor provide energy for the
completion of their replication.

Viral DNA or RNA encodes protiens

that mediate their own replication
inside some host cell.

F-7
 II. Viroids non-living entities

https://en.wikipedia.org/wiki/Viroid#/media/File:PSTviroid.png

Infectious particles that infect plants, but one viroid is known

to be the causative agent of hepatitis d in humans .
Viroids consist of a small circular RNA molecule
(usually single-stranded) several 100 nucleotides in
length).
- lots of complementary base-pairing

Unlike viruses, RNA of viroids code for any proteins.

Host cell’s RNA polymerase II enzymes do not new viroids
using the original viroid’s RNA as a template.
Spindle tuber disease of potatoes was the first viroid to
be recognized and studied by plant pathologists.
- appearance of other viroid diseases in our crops has
occurred in recent decades?

Viroids do not have cellular -

structure. No proteins

Do not carry out metabolism

Can not replicate themselves
Largest viroid 399 nucleotides long and smallest is
246 nucleotides in long.
Their genome is ten fold smaller than that the smallest
known RNA virus.
- considered to be the minimalist plant pathogen.
Spread by vegetative prroagules, mechanical damage, seeds,
III. Prions non-living entities

- Are glycoproteins/misfolded
forms
.

-- no
without
DNA cellular
or RNA http://apbio2-chs-09.wikispaces.com/Viruses.+Viroids,+Prions
structure Responsible for transmissible
- can’t metabolize
spongiform encephalopathies (TSE) in
a variety of mammals.
- infectious agent BSE bovine
encephalopathy of cattle
causing spongiform disease (CJD) and
- in humans, causes variant Creutzfeldt-Jakob
other human diseases such as kuru in the Fore tribe in Papua New
Guinea.
- other prion diseases include scapic in sheep and chronic
wasting
“It was known as mad cow disease, or Creutzfeldt-Jakob
disease, which increased dramatically in1996; 230 people have
died
from it”. 11/07/2019

Burning bodies of
cattle from infected
herds in Europe
Disease has a long incubation period (several
years).
Prions cause misfolding of normally folded proteins into
prion proteins in the central nervous system.
Prions aggregate extracellularly in the brain forming amyloid

fibrils which kill neurons in nervous tissue.

Disease spreads to new hosts by horizontal transmission,
mainly by ingestion of infected meat or via cornea
transplants.

Prions create holes

in brain tissue
giving it a spongy

architecture
https://en.wikipedia.org/wiki/Prion

Cook or freeze them, disinfect them, pressurize them, irradiate them

Although prions are not made of nucleic acids, they
can change and evolve.

How they do this is unknown.

Conclusion: viruses, viroids and prions are not living
entities.
Because they:
- Are not cellular in structure
- do not consist 4 types of the biomolecules of
life

- can not reproduce on own

- can not obtain energy from their external

environment.

However, they all have genetic material and their

populations can evolve.
 Biodiversity
It is a measure of the variety of life within a defined
location.
Three basic levels of
biodiversity:
Biodiversity is often described on three levels:
1) ecosystem diversity describes the variety of
habitat present, natural communities and
ecological processes in the biosphere.
2) species diversity is a measure of the
number of species and the
number of of each species present in a region.
3) genetic diversity refers to the total amount of genetic
variability present in all species. It refers to the genetic
variation between species and variation between
individuals within the same species.
Some also include:
4) cultural diversity is an considered an additional level by
Diversity of life ----> biological diversity or
biodiversity
Estimates of 2 - 10 million
species.
Exact number of species not known - why ?

1) Species counts biased by our tendency to study certain

organisms more than others
Group Species known Estimated species not
in the world species in the known
world

Nematodes 25,000 500,000 95%

Birds 9,900 10,000 1%
https://en.wikipedia.org/wiki/Nemato

extensively studied Nematodes (roundworms)

are a poorly studied
group & consequently we
have little grasp of how
diverse this group may
be.
Other possible reasons why a taxonomic group is poorly
known:
2) Habitat type (e.g. deep-sea), geopolitical location or endemism

makes them difficult to collect

- endemism – belonging exclusively or confined to a
Particular place .
3) Small size of the organism. Difficult to find.

4) Morphology of different species so similar they are

difficult to discriminate from each other. Called
sibling species.
6) Rare
5) Somespecies
internalare
parasites
difficultare hard
to find.
to locate in their host. Recently discovered “zombie
fly” parasite on honey bees
7) Taxonomy of a group has not been well worked
out.
The extreme opposite of endemism is a consmopolitan
distribution.

peregrine falcon
distribution of the peregrine falcon

Obviously, larger cosmopolitan species are typically well-

known.
Our knowledge of biodiversity of both fossil and extant species
does increase each year with the discovery of new species .
What Is The Best System To Keep A Record Of All The
Described
Species?
 Systematics
Scientific study of kinds & diversity of
organisms and the relationships Systematics
among them = discipline of
systematics
3 sub-disciplines

Taxonomy Nomenclature Phylogenetics

Greek words: Latin words: study of the
taxis = nomen = Evolutionary history or
arrangement name calare relationships
nomos = law = to call of organisms
theory & practice process where scientific names are
of calssifying produced for taxa at all hierarchal levels to
organisms into provide a common ground in which biologists
Taxa within a can communicate about specific taxa
hierarchy of Life
Classification
Aim of taxonomists is to put taxa in proper order and
provide stable names for them.

Taxon - …“group of one or more populations of an organism

or organisms seen by taxonomists to form a unit”.

-… “usually known by a particular name and given a

particular ranking ”….
https://en.wikipedia.org/wiki/Taxon
I. Nomenclature What is its name ?
What type of animal in this ? whistle-pig
woodchuck
Mammal groundhog
Rodent marmot

common names

https://en.wikipedia.org/wiki/Groundhog
Marmota monax scientific name

“digger” (American Indian

word)

Latinized version of Italian word

marmotta = mountain
Who devised the system of biological nomenclature ?
mouse
https://en.wikipedia.org/wiki/Marmo
 Carolus Linneaus (18th Century)
- Swedish botanist
- produced a complex system
for:
(1) species names
(2) taxonomic hierarchy
1758 - established a system of naming
organisms (binomial nomenclature )
1707-1778

Rules:
- each type of organism has only one name
- no two kinds of organisms should bear the same
name
- two part name - (Binomen ):
(i) Generic or genus name
(ii) Specific epithet (“trivial name”)
Binomial nomenclature:

Binomen written in italics or underlined Marmota

monax

Marmota monax Scientific name

name
begins with a Binomens are
Marmota monax UL
19.jpg
capital, the Latinized
Common names begins in lower
whistle-pig case
woodchuck
groundhog
marmot
Changes in scientific names

Mus monax Linnaeus, 1758

Authority and year

Marmota Blumenbach,
1779
Brackets to indicate change

Marmota monax (Linnaeus, 1758)

Authority
Written in italics or
underlined
1. Originally described by Linnaeus in 1758 as Mus monax .
2. In 1779, Johann Blumenbach created the genus name
Marmota
and transferred monax from genus Mus to genus
Marmota.
Changes in scientific names

Mus monax Linnaeus, 1758

Presence of brackets around Linnaeus

indicates monax was placed in
another genus by another taxonomist
at some later time.

Marmota monax
(Linnaeus, 1758)

Marmota Blumenbach, 1779

Blumenbach is the authority for the but Linnaeus is still
the for the species name.
Provided there is agreement among taxonomists, the most
recent revision of the a name is accepted as the name to be
used in all publications and discussions relating to
that particular species.
3 types of
mammals (class
Mammalia)

wikipedia

Live birth

lay eggs
(no live birth)
 _
In placental mammals the fetus is carried within its
mother’s uterus and nourished by a more complex
chorioallantoic placenta until a relatively late stage of
development.
Gestation is
long._
Are three
embryonic
membranes in the Embryo of a
reptile, bird, or egg
land egg:
laying mammal
Amnion
Chorion
Yolk sac https://bio.libretexts.org/
In marsupials, on the other hand, the fetus spends only a
short time nourished by a yolk sac placenta before
birth. The juvenile at a very immature stage of
development.
Gestation is short.
The juvenile in marsupials is nourished and protected for
a long period of time in its mother’s pouch .
Gestation is the period of time between conception and birth .

Monotremes are egg-layers, so they lack a placenta. No

gestation.

endemism

chorioallantoic
placenta
https://commons.wikimedia.org/wiki/File:2910_The_Placenta-02.jpg
3 types of
mammals (class
Mammalia)

Placenta (chorioallantoic)

wikipedia

Live birth Live birth

yolk sac placenta

Mammary

Marsupials have a yolk sac placenta

lay eggs
(no live birth)
Class Mammalia

How did it get

its scientific
name ?

https://en.wikipedia.org/wiki/Platypus

Ornithorhynchus anatinus (Shaw,

1799)