Ch. 20: Viruses, Bacteria, and Archaea
Classified based on two main features:

Whether genetic material is DNA or RNA and whether it is single- or doublestranded

Clustering by size and shape, like the KPCOFGS for truly living organisms
Structure of Viruses
a) Viral Genomes

may be double-stranded DNA, single-stranded DNA, double-stranded
RNA, or single-stranded RNA

linear or circular

may have 3 genes to 100 genes
b) Capsids and Envelopes
o Capsid = protein coat that encloses the viral genome
o Envelope = membrane that cloaks some viral capsids
o Made from polysaccharides
Viruses Can Reproduce ONLY Within a Host Cell = Obligate Intracellular Parasites
Host Range = Limited number or range of host cells that a virus can infect
o Viruses recognize host cells by a complementary fit between external viral
proteins and specific cell surface receptors
o Some have broad host ranges = include several species
(ex. Rabies)
o Some have narrow host ranges = include only one species or one cell type of
one species (ex. Influenza or HIV)
Viruses Mutate Very Quickly

Small amount of RNA or DNA

Have NO DNA or RNA Repair Enzymes
o Ex. HIV is hard to make a cure for because all of the billions of virions in
an infected person will not be the same  at least one will find a way to
resist the treatment
Viral Life Cycles Involve:
o Infecting the host cell with viral genome
o Viral genes use the host cell’s enzymes, ribosomes, tRNAs, amino acids, ATP,
and other resources to:
o
make copies of the viral genome
o produce viral capsid proteins
o Viral nucleic acid and capsid proteins assemble spontaneously into new virions, a
process called self-assembly
3 Patterns of Viral Genome Replication
1) DNA  DNA
-
uses host’s DNA Polymerase
2) RNA  RNA
-
uses RNA Replicase = enzyme that uses viral RNA as a template to
produce complementary RNA
3) RNA  DNA  RNA
-
Uses Reverse Transcriptase = an enzyme that transcribes DNA from an
RNA template
BACTERIOPHAGES (and their Reproductive Processes)
THE LYTIC CYCLE
Virulent bacteriophages reproduce only by a lytic replication cycle
Virulent = phages that kill their host
1) ATTACHMENT
-
Phage recognizes and binds to host cell by specific receptor sites
2) PENETRATION
o Phage contracts sheath and injects DNA into host cell
3) BIOSYNTHESIS
o Hydrolytic enzymes destroy the host’s chromosome
o Host cell begins to transcribe and translate viral genome
o Phage’s own DNA is protected because it contains modified cytosine
(C) not recognized by the enzyme.
o Phage genome directs the host cell to produce viral components: DNA
and Capsid proteins
4) MATURATION
o New viral components assemble into new virions
5) RELEASE
o Osmotic swelling lyses the cell, releasing new phages
o Released virions can infect nearby cells
o Takes only 20 minutes at 37oC
Restriction Enzymes = Naturally occurring bacterial enzymes that protect bacteria
against intruding DNA from other organisms
-
Cut foreign DNA into small segments
-
Bacteria have them for defense against phages (Don’t always work.)
THE LYSOGENIC CYCLE
Temperate Viruses = viruses that can integrate their genome into a host chromosome and
remain latent (inactive) until they initiate a lytic cycle
Lysogenic Cycle = a viral replication cycle that involves the incorporation of the viral
genome into the host cell genome
1) ATTACHMENT
2) PENETRATION
3) INTEGRATION
o DNA inserts by recombination into a specific site on the bacterial
chromosome and becomes a prophage
o Prophage = a phage genome that is incorporated into a specific site on the
bacterial chromosome
o Prophage genes are copied along with cellular DNA when the host
cell reproduces
o May be carried in host chromosomes for many generations/years
o Most prophages are inactive
o Some may still be actively producing harmful proteins/toxins

Ex. Strep throat bacteria with a certain prophage cause
scarlet fever

Ex. Botulism is in all raw eggs, but usually it only causes
food poisoning if the right prophage is in it
o Eventually, a prophage will leave the bacterial chromosome and
may begin the lytic cycle  usually when environmental
conditions trigger it
ANIMAL VIRUSES
Reproductive cycles of animal viruses

Have a Viral Envelope external to the capsid
o Helps the virus infect host cells
o Made from host cell’s plasma, ER, or Golgi membrane
o Is a lipid bilayer with glycoprotein spikes (made from the virus’ genome)
protruding from the outer surface.

Replication cycles characterized by:
1) ATTACHMENT: Spikes attach to receptor sites
2) Entry: Envelope fuses with the plasma membrane, the entire virus (capsid and
genome) is transported into the cytoplasm by receptor-mediated endocytosis.

Cellular enzymes uncoat the genome by removing the protein capsid
from viral RNA.

May or may not insert its DNA into the host chromosome  provirus
3) BIOSYNTHESIS:

May enter the lytic cycle (ex. Ebola) or lysogenic cycle (ex. HIV or
herpes virus (nature of herpes infections)

Same as before, but also includes production of glycoprotein spikes,
which are sent to and displayed on the plasma membrane
4) MATURATION & RELEASE.
Virions are enveloped with host’s plasma membrane as they push out through
the cell’s surface  budding
Retroviruses

Retroviruses = (Retro = backward) RNA virus that uses reverse transcriptase to
transcribe DNA from the viral RNA genome.
o Ex. HIV, the virus that causes AIDS
Virus enters cell and goes through reverse transcription
↓
Integration = viral DNA enters the nucleus and
inserts itself into host chromosomal DNA as a provirus
↓
Viral RNA and protein synthesis occur and MAY:
Produce new virions
Cause expression of
oncogenes, if present
Capsid assembly and
Cancerous State
release of new virions
Effects of viral diseases in animals
Viruses cause disease by:

Damaging or killing cells.

Being toxic themselves or cause infected cells to produce toxins.
o Cause varying degrees of cell damage depending upon regeneration ability
of the infected cell.

Be indirectly responsible for disease symptoms. Fever, aches and inflammation
may result from activities of the immune system.
Emerging viruses

Viruses that are suddenly infecting large numbers of humans

Not likely to be new viruses, but often mutated versions of older ones

Can arise if an existing virus:
1) Mutates
2) Spreads from one host species to another
3) Spreads from a small population to become more widespread
4) Combines with another, similar virus to create a new virus

Ex. Possible Bird Flu Epidemic
o Concern that the H5N1 bird flu strand will join in a human with
the H5N1 human flu virus.
o If the two fuse, it would have spikes from both, allowing it to
spread through the air, doorknobs, etc.

H spikes allow viruses to bind to receptors (16 types)

N spikes attack host plasma membranes to allow mature
viruses to exit (9 types)
Viruses and cancer
Some tumor viruses cause cancer in animals.
Some viruses can transform normal cells into cancerous state.

Ex. Retroviruses, papoviruses (ex. HPV), adenoviruses and herpesvirus

May be due to loss of gene control when proviruses insert themselves in a
regulatory region of host DNA  is permanent, never excises
Plant viruses are serious agricultural pests
Many of the plant viruses:

Stunt plant growth and diminish crop yields

Are RNA viruses.

Most plant viral diseases have no cure
Viroids and prions are infectious agents even simpler than viruses

Viroids = small, naked, circular RNA molecules that do not encode protein
o Infect plant cells

Prions are animal cell pathogens that are proteins
o Prions are defective versions of normally occurring cellular proteins.
o When prions infect normal cells, they convert the normal protein to the
prion version.
o Triggers a chain reaction that increases their numbers
o Many cause neurodegenerative diseases

Ex. Transmissable Spongiform Encephalopathies (TSEs), like Mad
Cow Disease