VIRUSES, BACTERIA, ARCHAEA
and PROTIST
Viruses
• Virus = (Latin) Poison
• Viruses are NOT considered to be living.
• do not metabolize, respond to environment, or
reproduce on their own.
• Viruses are NOT cells.
• no nucleus, organelles, or cytoplasm
• Do have features in common with life
• Have genetic material (DNA or RNA)
• Evolve
Viruses
• Extreme genetic diversity of viruses suggest
they do not have a single common ancestor
• Not part of any domain or kingdom
• Viruses assigned species, genera, and
families but no taxonomy higher than order
• All viruses:
• Contain genetic material (DNA or RNA)
• Have a protein coat (Capsid)
Viruses
• Tiny, infectious agents that:
• have a nucleic acid core (RNA or DNA, but not
both).
• have a protein coat (capsid) made of capsomers.
• may have a lipid rich envelope.
• This structural unit is called a virion (a single viral
particle).
Envelope
• Viral envelope is composed of lipids carbohydrates
& proteins which is derived from the host.
• Proteins are what allow for attachment to host.
• Enveloped viruses need envelope to initiate
infection.
HIV (enveloped virus)
Adenovirus (naked virus)
Virions
• Diameter of virus
particle ranges from
20-200 nm
(average 80 nm)
• Average diameter of
bacterial cell is 1,000
nm
• Average diameter of
eukaryotic cell is
10,000 nm
Retroviruses
• RNA viruses
• Uses Reverse Transcriptase enzyme to
copy RNA back to DNA
• Causes a rapid mutation rate
• Vaccine must be updated every year.
Viral Pathogenicity
• Pathogenicity – ability to cause disease. (infection)
– depends upon the ability of the virus to infect its host
– and the condition of host defense system.
Viruses have a specific host range. The host must
have the target receptors or molecules.
- range may be broad (specific class of organisms)
Ex. rabies virus infects most mammals
- range may be narrow (specific species)
Ex. small pox virus infects humans only
- range may be very narrow (specific cell line)
Ex. Human immunodeficiency virus infects only helper T cells in
humans
• Certain hosts develop illness.
• Certain hosts show no symptoms - function
as reservoirs.
Ex. pigs & ducks serve as reservoirs for influenza (flu)
viruses.
Influenza can jump from either animal to humans (zoonosis).
Mice serve as reservoirs for the Hantavirus. Mice will remain
healthy, humans that come in contact with saliva, urine or
feces from the mice will become infected.
Viral Replication
1. Attachment
– Attach to host cell by adhering to surface molecule
2. Penetration
– Different methods – enzymes create hole, endocytosis
3. Synthesis
– Host cell provides all resources and machinery
– Viral DNA transcribed and translated by host ribosomes
4. Assembly
– Capsid subunits join, genetic information packaged
5. Release
– May burst cell or enveloped viruses bud from cell over
time
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•
Damages or destroys host cell resulting in disease
Time between infection and cell death varies
Lytic or lysogenic
• Lytic infection (most viruses)
– Virus enters cell, immediately replicates, causes
cell to lyse releasing new viruses
• Lysogenic
– Virus enters cell
– Inserts into host DNA as prophage
– Remains latent without causing symptoms
• Copied along with host DNA into new cells
– Some signal causes prophage to emerge and
revert back to the lytic stage.
Lysogenic Stage
Some viruses enter a period of dormancy after
invading a host cell this is called the latent period
• integrate into the host chromosomes and are replicated
each time the cell divides
• may alternate between periods of inactivity & recurrent
infections.
• signal the host cell to replicate this may transform host cell
into a cancer cell.
Ex. Herpesvirus & Epstein-Barr virus
Host defenses
Bacteria use restriction enzymes to destroy viral DNA
by chopping it to pieces.
Animal cells employ an immune system:
• Antibodies coat viral particles so they can’t adhere to
target cells.
• Certain virus-infected cells rupture before progeny viruses
can be released.
• Virus-infected cells release chemicals that protect
surrounding uninfected cells.
Combating Viruses
• Difficult
• Once they infect the cells and incorporate their
DNA, our immune system can not identify them.
• The cells replicate the viral DNA which results in a
cell line that is infected with viruses.
• Very few anti-viral drugs and they are not very
affective
• Once you get a virus you will always have the virus.
Drugs
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•
•
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Antibiotics do not work against viruses
Difficult to develop drugs against viruses
Complicated by genetic variability of viruses
Vaccination is our most potent weapon
– “Teach” immune system to recognize
components of invader
– When the individual is exposed to the virus, the
body recognizes it, and destroys it before it
enters the cells.
– Smallpox and polio vaccinations highly effective
– Unable to develop vaccinations against all
viruses
Other Infectious Agents
1. Viroids - infectious RNAs that affect plants.
–
Double stranded RNA, No protein coat
Ex. Avocado sunblotch, Tomato bunchy top, Chrysanthemum
stunt disease
2. Prions – Proteinaceous infectious particle or PrP
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–
–
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They cause proteins to change shape (conformation)
Cascading effects
Infectious proteins associated with transmissible
spongiform encephalopathy that occurs in 80 different
mammals.
These are not detected by the immune system and will
cause the cells to die.
Ex. Scrapie, Kuru, Creutzfeldt-Jakob disease, mad cow
disease
Overview
BACTERIA AND ARCHAEA
• We group these together as prokaryotes,
because they both lack a nucleus and any
compartmentalization, but they are not very
closely related based on DNA sequence.
• The Archaea is more closely related to
Eukarya (Plants and Animals) than they are
to bacteria.
Cladogram
Bacteria
Archaea
Eukarya
• This information came from resent DNA
sequence data
Bacteria and Archaea Shared Characteristics
• Both have a cell membrane
• Both have ribosomes
• Both have a nucleoid region that contains a single
circular chromosome
• Both have a cell wall
• Both are single celled organisms
Comparing
Bacteria and
Archaean
Internal Structure
• DNA
– One circular chromosome
– Located in nucleoid (nuclear region)
• Plasmids – small circular pieces of DNA
– Code for drug or toxin resistance, cause disease,
alter cell’s metabolism
– Used in recombinant DNA technology
– Accounts for most antibiotic resistance
• Ribosomes structurally different from
eukaryotes and from each other
– Some antibiotics exploit this difference
– Ex. Streptomycin
Cell wall
• Rigid structure outside cell membrane
– In bacteria it is composed of mainly
Peptidoglycan
– In archaea it is composed of mainly
pseudopeptidoglycan
• Gram stain differentiates between 2 major
groups of bacteria which is based on cell
wall structure
– Gram-positive – appear purple due to thick
peptidoglycan layer
– Gram-negative – appear pink due to thinner cell
walls and an outer membrane covering
• Outer membrane is what causes the inflammation
• Glycocalyx
– Capsule or slime layer
– Sticky layer outside cell wall
– Attachment, resist drying, protection
from immune system
• Pili
– Short, hair-like projections
– Adhere to objects
– Sex pili transfer DNA
• Flagellum
– Whip-like extension to move cells
– Not homologous to eukaryotic
flagella
– Taxis – move toward or away from
stimulus
– Ex: Chemotaxis, phototaxis, geotaxis
• Endospores are thick walled structures that
form around DNA & a small amount of
cytoplasm.
• Allows bacteria to survive harsh conditions.
• Endospores can withstand boiling & drying.
• Can be killed by 10-15 minute superheated
steam treatment. (Autoclaved)
– Clostridium botulinum
• Botulism
• Common in home canned foods due to improper
sterilization
– Bacillus anthracis
• Anthrax
Classification
• Traditionally relied on observable
characteristics
– 3 common shapes – cocci (spherical), bacilli
(rod-shaped), and spirilla (spiral)
– Cell arrangements – pairs, clusters (staphylo-),
or chains (strepto-)
– Gram stain (positive or negative)
– Other stains for flagella, endospores, or
glycocalyx
• Cocci - have spherical shaped cells
• Bacilli - have rod shaped cells
• Spirilla - have spiral shaped cells
• Based on Staining Characteristics
• Gram positive (+) bacteria
Cell walls have thick peptidoglycan layer; stain
purple.
• Gram negative (-) bacteria
Cell walls have thin peptidoglycan layer & an
outer membrane; stain pink.
Metabolic Pathways
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Carbon source
– Autotrophs – acquire carbon from inorganic sources (CO2).
– Heterotrophs – carbon from organic molecules
Energy source
– Phototroph – energy from the sun
– Chemotroph – oxidize inorganic or organic chemicals
Oxygen requirements
– Obligate aerobe – requires oxygen
• Ex. Bacillus
– Obligate anaerobe – oxygen is toxic
• Ex. Clostridium tetani
– Facultative anaerobe – can live with or without oxygen
• Ex. Escherichia coli & Salmonella
Modern Methods of Classification
Based on molecular data; groupings reflect
evolutionary relationships.
Ribosomal RNA (rRNA) sequences of organisms
are compared to identify signature sequences.
Signature sequences are short stretches of
nucleotides that are unique to certain types of
organisms.
Molecular data show Bacteria and Archaea
have different:
• genetic sequences and antibiotic sensitivities
• cell wall components and membrane lipids
• numbers of introns and repeated genetic sequences
• cell shapes
Vertical Gene Transfer
• Bacteria Reproduction
• Use binary fission
• Resembles mitosis; however, it is different
because it lacks spindle fibers & many types
of proteins that are associated with the more
complex linear chromosomes of eukaryotic
cells.
• Chromosomes attaches to the cell
membrane
Transformation
Transduction
Conjugation
Domains
• Domain Bacteria
– At least 23 phyla
– Very diverse – photosynthetic, nitrogen cycling,
medically important, source of antibiotics
• Domain Archaea
– “extremophiles” – first found in extremely hot,
acidic, or salty environments
– More being discovered in moderate
environments
– Often thought of as the most primitive
– 3 phyla
Harmful effects of Bacteria
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Only few species of bacteria are harmful to man
because they are pathogenic. (1%)
Bacterial infections may be spread by:
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Air (inhalation)- Legionella pneumophila (causes
legionellosis, a form of pneumonia).
Arthropods (bites)- Yersinia pestis (causes bubonic
plague) is transmitted to humans by rat fleas.
Direct Contact - Neisseria gonorrhoeae (causes
gonorrhea) is transmitted by sexual contact.
Food & Water (ingestion)- Vibrio cholerae (causes
cholera); Salmonella enteritidis (causes food
poisoning).
Abrasions on the skin - Staphylococcus aureus
Why they are harmful
• Pili attach (anchor bacteria)
– Enzymes secreted destroy tissue.
• Ex. Helicobacter pylori ( causes ulcers)
– Toxins produced destroy tissue.
• Ex. Bacillus anthracis (causes anthrax)
Antibiotics
• Inhibits cell wall production
– Penicillin
• Disrupting cell membrane
– Polymyxin
• Inhibits protein production (ribosomes)
– Erythromycin
• Inhibits transcription (RNA polymerase)
– Rifamycin
• Inhibits enzymes (metabolic pathways)
– Sulfanilamide
Beneficial effects of Bacteria
• Most prokaryotes are beneficial in that
they:
• break down organic wastes & dead organisms.
• cycle chemical elements (oxygen, nitrogenfixing) between organisms & the environment.
• are used in the production of food. (vinegar,
pickles, sauerkraut, olives, yogurt, cheese)
• are used to mass-produce certain non- food
items. (vitamins, enzymes, ethanol, acetone,
human insulin & blood clotting factors)
• are used in water and waste treatment.
• are used in bioremediation. (certain microbes
degrade oil, while others remove heavy metals
from water)
Overview
Protists
• The Kingdom Eukarya they are eukaryotes-meaning they have a
nucleus and membrane bound organelles.
• Multiple Kingdoms
• Some are plant like they are autotrophic, contain chloroplasts
filled with chlorophyll. Ex. Algae and Euglena
• are aquatic
• are heterotrophic and decompose Ex. Slime mold
• are parasitic
• Protozoans are another type of heterotrophic protist some cause
disease Ex. Trichomonas
• Amoeba, Paramecium are examples
• Basically any ekaryote not classified as Plant, Animal or Fungi
was classified as a Protists