Viruses/viroids/prions

Let’s return- are viruses dead or alive?

• 1. Living things must maintain homeostasis
• In earlier drafts of criteria for life, the requirement was that
living things must be made of cells. Viruses are not made out
of cells.
• A single virus particle is known as a virion, and is made up of
a set of genes bundled within a protective protein shell called
a capsid.
• Viruses do not have nuclei, organelles, or cytoplasm like cells
do, and so they have no way to monitor or create change in
their internal environment.
• Verdict: Fail
• 2. Living things have different levels of
organization.
• Life is a complicated idea, and live organisms reflect
that complexity in their structure. Smaller building
blocks come together to make a larger product.
Viruses certainly do this. They have genes made from
nucleic acids and a capsid made of smaller subunits
called capsomeres.
• Verdict: Pass
• 3. Living things reproduce.
• Viruses definitely multiply.
• Since viruses don’t have organelles, nuclei, or even
ribosomes, they don’t have the tools they need to copy their
genes, much less create whole new virions. Instead, viruses
enter living cells and then hijack the host’s cellular equipment
to copy viral genetic information, build new capsids, and
assemble everything together.
• We use the term replicate, instead of reproduce, to indicate
viruses need a host cell to multiply.
• Verdict: Maybe
• 4. Living things grow.
• Viruses manipulate host cells into building new
viruses which means each virion is created in its
fully-formed state, and will neither increase in size
nor in complexity throughout its existence.
• Viruses do not grow.
• Verdict: Fail
• 5. Living things use energy.
• Creating new virion units is a major undertaking,
from building nucleic acids to putting capsids
together – that costs a lot of energy.
• However, all the energy that goes into this
construction comes from, you guessed it, the host.
• Verdict: Maybe
• 6. Living things respond to stimuli.
• Whether viruses respond to their environment is one of
the trickiest questions to answer. A response to a stimulus
is defined by an almost immediate reaction to some
change in the environment.
• While they don’t change behaviors in response to touch or
sound or light the way that humans, bacteria, or sea
sponges might, there has not been enough research done
to definitively say that viruses do not respond to anything.
• Verdict: Unknown
• 7. Living things adapt to their environment.
• Adaptation and evolution happen through unintentional changes (mutations)
that are advantageous to an entire species. Viruses definitely adapt to their
surroundings.
• This ability to adapt is what makes human immunodeficiency virus (HIV) as
hard to treat as it is. HIV mutates quickly because it makes frequent mistakes
while replicating its genome. Because the virus is constantly changing, it makes
it very hard to design drugs and vaccines against it. One drug might prevent a
large number of virions from replicating, but just a few will be unaffected.
• Those surviving virions will continue to infect more cells, making copies of the
resistant strains.
• This is the same concern we currently face when trying to make a vaccine to
battle covid-19. If viruses replicate rapidly, mistakes (mutations) are inevitable,
the virus WILL change and therefore a vaccine can now be guaranteed to get all
strains of the virus 
• Verdict: Pass
• Where does this leave us? Are viruses alive or dead? Well, we know
they’re not dead. Death is what happens when a living organism stops
performing biological functions, and for the moment we’re only
interested in the active particles. So were they ever alive?
• Most biologists say no.
• Viruses are not made out of cells, they can’t keep themselves in a
stable state, they don’t grow, and they can’t make their own energy.
Even though they definitely replicate and adapt to their environment,
viruses are more like androids than real living organisms.
• Just like crazy killer robots, viruses are created fully formed, and rely
on host materials to build and power themselves!
• If a virus isn’t alive, does that affect how we deal with viral infections? Absolutely.
Antibiotics, for example, are used to treat bacterial infections, and are useless at
dealing with a viral infection like the flu or chickenpox. Antibiotics target certain parts
of bacteria in the hopes of killing them; with viruses it’s hard to kill something that
isn’t quite alive to begin with. Instead of destroying the virus, antiviral medicines try
to shut off the replication cycle, like shutting down the android production line.
• What happens if a virus infects another virus? Scientists found a bacteria-sized giant
virus which they named mamavirus. Upon further study, it turned out that this giant
virus actually had a smaller virus associated with it.
• When mamavirus infected amoeba, it created a giant virus factory, whose machinery
was then hijacked by the smaller virus. Some scientists have pointed out the fact that if
a virus can get sick, then it is should be considered a living thing! What a world we
live in!
What is a virus?
• small particle
• infects living cells in order to replicate
▫ animals, plants, fungi, bacteria
Phylogeny and Origin
• Classification and Phylogeny:
• Classified as non-living as they do not have key characteristics of
cells, except for the fact that they reproduce (although replicate is
the more ACCURATE term to use)

• Origin of Viruses:
• Obviously, there is no fossil evidence of viruses and their
evolutionary history, therefore, scientists can only make educated
guesses based on no actual proof
• The most accepted theory is:
▫ viruses developed from detached fragments of genetic
material from other cellular organisms over time
 Virus Structure
Viruses have a much simpler structure than most
living organisms

They consist of:

• a protein coat that is part of the
• head, called a CAPSID
• a nucleic acid core
• a tail (bacteriophages)
 Viral Structure
the CAPSID:
- the protective protein coat of the virus
- protein “spikes” allow recognition of host cell
- Makes up 95% of the virus
- gives the virus its particular shape
- is sometimes covered by a lipid membrane (HIV)
 
the NUCLEIC ACID core:
- can be RNA or DNA, but not both, unlike living organisms, which contain both
- can be single or double-stranded, depending on the virus
 
the TAIL:
- found in bacteriophages; phages are a category of viruses that infect and destroy
bacterial cells
- functions in attachment to bacteria
- Can often contract and shorten to help inject the nucleic acid core into the bacterial
cell
 
DNA Monomer
PHOSPHATE
O

O- P O CH2

O- NITROGENOUS
BASE
A, T, G, C
DEOXYRIBOSE

OH
RNA Monomer
PHOSPHATE
O

O- P O CH2

O- NITROGENOUS
BASE
A, U, G, C
RIBOSE

OH OH
 Variations in viral structure
Helical Icosahedral Spherical Bacteriophage
rod-shaped capsid polyhedral capsid surrounded by icosahedral “head” &
with 20 triangular membrane envelope protein “tail”
faces
 Viral Diversity and Specificity
 viruses can be highly selective: some attack only bacteria, some only
animals, some only plants
 the range of types of tissues or cells that can be infected by a virus is
called the “host range”
 Phages (viruses that attack bacteria) usually have a very LIMITED host
range
 many animal and plant viruses, however, have a BROAD host range
o the rabies virus can infect many species, including rodents, dogs, and
humans
 of course, there are exceptions:
o HIV attacks only the cells of the immune system
o SARS attacks only the cells of the respiratory system
Bacteriophages do NOT enter the host cell when they infect them.
ONLY the DNA or RNA gets injected into the bacterium, but their protein
capsule remains outside of the cell.
Plant and animal viruses enter the cell completely, including the protein
capsule.
How viruses enter plant and animal cells:

2) enter plant cells through tiny rips

in the cell wall
3) enter animal cells by endocytosis
 Viral Replication
• Viral replication involves FOUR
steps:
• 1. Attachment
• 2. Synthesis
• 3. Assembly
• 4. Release
1. Attachment:
 the virus chemically recognizes a host cell and attaches to it
 either the whole virus, or ONLY its genetic material (DNA or
RNA) enters the cell
 
2. Synthesis:
 this is the replication of the viral genome
 molecular information contained in the viral DNA (or RNA)
takes over the host cell and directs it to replicate new viral
components:
o nucleic acids, enzymes, capsid proteins, other viral proteins
o the components are created separately
3. Assembly:
• the newly created components, viral genomes,
enzymes, and proteins, are brought together
and assembled into new viruses
 
4. Release:
• the newly formed viruses cause the cell to lyse
and are released
• the host cell dies
Viral Replication
• virus enters cell
• forces infected cell to use its
own energy and resources
to build new viruses
▫ DNA replication
▫ protein synthesis for capsid

• viruses assemble inside

infected cell
• release into environment
 Viral Replication
1. Lytic cycle
- the lytic cycle can be as short as 25-45 mins. and produce as many as
300 new viral particles
 - in the lytic cycle the host cell undergoes LYSIS (breaking/rupturing)
- Viruses that go through the lytic cycle are considered to be VIRULENT
phages

2. LYSOGENIC CYCLE
- A replication cycle that does NOT cause the rupturing of the host cell
- Viruses that go through the lysogenic cycle are called TEMPERATE
phages
 
 Viral Replication Con’t...
• in a lysogenic cycle, the virus co-exists with the cell similar to the lytic
cycle, the virus attaches to the bacteria and injects its genetic
material
 
However…
• instead of taking over the cell, its nucleic acid becomes
INTEGRATED into the bacterial DNA and acts as another set of
genes on the bacterial host chromosome
 
• then, once the bacteria reproduces, the viral genome is reproduced
and passed on to all the daughter cells
 
 Viral Replication Con’t...
• When the virus is in this stage of the lysogenic cycle, it is said to be
DORMANT (asleep)
 
• this viral genome is still dangerous because it can become
ACTIVATED by an outside stimulus, such as:
• damage to the DNA
• changes in temperature
• loss of necessary nutrients
 
• if the viral genome becomes activated, the virus will move on to the
lytic cycle and the virus becomes virulent again
 http://
highered.mheducation.com/sites/0072556781/student_view0/ch
apter17/animation_quiz_2.html

Lytic Cycle: Bacteriophage Example

Release causes
lysis of
bacterial cell
Lysogenic Cycle: Bacteriophage Example
Phage DNA is
incorporated into host
genome.
▫ replicates with it
▫ forms a “prophage”

Environmental stress
triggers induction:
1. excision of
viral DNA
2. entry into lytic
phase
(rapid reproduction)
Comparison

Classification of phages…
• “virulent phages” - replicate only
through the lytic mode
e.g., T4 phage
• “temperate phages” – alternate
between lysogenic and lytic
e.g., lambda phage
Viruses in Animals
• all have envelope
▫ viral proteins on outside
▫ bind to receptors on host cell
▫ allows entry to cell

• envelope proteins are specific for certain types

of cells:
▫ common cold (adenovirus) – respiratory tissues
▫ poliovirus – nerve cells
• Examples
▫ lytic: common cold, flu, covid-19, rabies
▫ lysogenic: herpes (cold sores), hepatitis B,
chicken pox

• lysogenic viruses are characterized by

asymptomatic periods with occasional flare-ups
Viruses are not affected by antibiotics.

• antibiotics target life processes that are performed

by bacteria; results in pathogen destruction
• viruses don’t have equivalent processes

• difficult to find targets for anti-viral medication

• inhibit binding to/entering host cells
• inhibit viral synthesis – genome, capsid assembly
• inhibit release of virus
Vaccination can prevent infection.
• A vaccine is made (Vaccination) (Infection)
from weakened or
killed forms of the
virus
• exposure stimulates
patient to produce
antibodies
• resistance or immunity
to subsequent
infection
Some viruses are helpful to humans.
• Bacteriophages – Prevalent in mucus
▫ kill harmful bacteria

• Biotechnology
▫ gene therapy
▫ vaccines
▫ biocontrol
 Helpful Viruses?
Gene Therapy
• gene therapy is a process by which viruses are used as vectors
(carriers) to carry altered DNA to defective cells in order to
CORRECT the disease or malfunction; so in this case, the virus is
used for GOOD
• to create a viral vector, scientists remove the viral genome and
replace it with the new gene to be transferred
• the vector is then mixed with growing cells in a laboratory
• the vector enters a cell and deposits the new gene in the genome of
that cell
• the new gene is then passed on to daughter cells when the altered
cell divides
• in the laboratory, scientists have had a 90% success rate using
this process
 Problems with Gene Therapy…
 

• this kind of procedure is only useful in cells that are

DIVIDING
• cells in the spinal cord and brain are no longer
multiplying, so they cannot be “fixed” using viral
vectors
• this means that paralysis, and neurological
diseases, such as Parkinson’s and Alzheimer’s
diseases, cannot be cured by this method
Prions are another type of
non-living pathogen.
• prion – infectious protein
• an abnormally folded
form of normal brain protein
▫ can convert normal proteins
into abnormal forms
▫ aggregation of
abnormal protein

• causes degenerative
brain disease:
▫ scrapie, mad cow disease,
Creutzfeldt-Jakob disease, kuru
• incubation period of 10+ years
▫ difficult to trace source of infection

• resists high temperatures and enzymatic digestion

▫ thought to be transmitted through food
Case study: Kuru
• epidemic in 1960’s
• Fore people of Papua New
Guinea
• symptoms: muscle tremors,
uncontrollable laughter, slurring
of speech, inability to swallow
• women and children most
affected

• genetic basis was ruled out

• anthropologists: funerary cannibalism was
common practice
Viroids are infectious RNA particles.
• pathogens of plants
• smallest infectious particles known; disc. 1971

example: potato spindle tuber viroid

▫ potatoes, tomatoes
▫ stunted growth,
colour changes,
elongated/cracked tubers
• short stretches of single-stranded RNA;
no protein coat
• use host cell to make copies
• don’t contain instructions to
make any proteins

• transmitted by mechanical methods:

contaminated machinery, tools,
pruning, seed, pollen
Evolutionary significance?
ancient relic of a world before DNA and protein
precursor to viruses
intermediate between inanimate matter, and life
Summary
• Viruses are infectious particles composed of a
DNA or RNA genome, surrounded by a protein
capsid. They lack the basic characteristics of
cellular, living organisms.

• Once they infect a cell, they replicate using

either the lytic mode or the lysogenic mode.
• Retroviruses have a unique method of
replication, due to their RNA genomes.

• Vaccination is an effective method for preventing

some viral infections.

• Other, non-cellular infectious particles are prions

and viroids.
Homework
• 1. Complete “virus homework” handout
• 2. Complete the “making a vaccine” worksheet.
Research 2 vaccines and take notes on how
they are made
• http://www.pbs.org/wgbh/nova/bioterror/vacc_nf.html