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week 5

Lab Report
(sections with a * MAY be done with
Introduce the topic you are about to present (1 paragraph 1 page)


What did you do? Step by step. Be specific and please number steps.

No interpretation here! Just tell me what you saw.

Photos are great

Paragraph form (again, no interpretation!)

Now you interpret what you found. Why do you think you obtained the results you obtained? Were you surprised to see
those results? Why or why not? Did anything unanticipated happen that may have altered your results? (Did someone
sneeze on your plate while it was open?)

Close the report by stating anything you would have done differently if you had to do it again or by suggesting another
experiment based on the results of this one.


Learning outcomes


Define criteria used to classify bacteria


Describe the components of a virus



Identify viral replication strategies for RNA viruses, DNA

viruses, and Bacteriophages


Explain how prions cause disease


Lytic cycle

Differentiate between plant-like protists and animal-like


Lysogenic cycle



Describe the characteristics of helminthes and the diseases

they cause


Compare and contrast different types of microorganisms


Create a microbe


Design and implement and experiment to examine microbial


Describe the characteristics of fungi and the diseases they


Taxonomy: a means of organization



Genetic features
Fossil records

Metabolic reactions
Genetic relatedness
Other properties

numerical taxonomy (for prokaryotes)

different characteristics are evaluated
if organism has the characteristic, its given a value of 1; if it doesnt
then it gets a value of 0
all the values are added together
organisms with similar values are considered more closely related
What characteristics might you wish to evaluate when dealing with bacteria?
-gram stain, anaerobe/aerobe, capsule, enzymes, etc.
*take a look at the handout!

Which characteristics are helpful in lab

Look at pp. 260-261 and then check out appendices on pp. 257-263 in
lab book for examples!

Difficult to classify
Fewer than 1% of known bacteria are completely classified from
domain to species
We know genus, species, strain/subspecies but its difficult to know
their entire evolutionary relationship in order to classify them

debate continues as to whether theyre alive or not as they have no
means of replicating their own genetic information
intracellular hosts required

genetic information in viruses

either DNA or RNA
never both!!!!

The nucleic acid core is either DNA or

RNA, not both!
The type and number of strands of
genetic info is a classification criteria.
The numberand arrangement of
capsomeres are another classification
criteria and helps to distinguish
between types of viruses.
A viron without an envelope is
considered naked.
Envelopes consist of host membranes
and expressed viral genes. Theyre
made of lipids, proteins, and
carbohydrates. Some may have
spikes made of glycoproteins that
extend from the viral envelope and
assist in recognition and attachment
to the host cell.

Viruses with envelopes are able to

more easily evade the hosts immune
system as they use host cell
membranes in their envelope.
However, naked viruses are harder to
kill with disinfectants as they do not
contain that layer in which to target.

range in size from
240nm (the size of
the smallest
bacteria) to less
than 30nm (the size
of a ribosome)

host cells
viruses need a host cell
the host range of a virus is the spectrum of hosts that a virus can
most viruses have a viral specificity limited to a certain species and
even specific tissues within a specific host
ex: HIV attacks human CD4 T cells
HPV infects human skin cells

viral classifications
viruses are classified based on:

type and structure of nucleic acid

method of replication
host range
other chemical and physical characteristics
such as arrangement of morphology

viral species
a viral species is defined as a group of viruses that share the same
genome and the same relationships with organisms
ex: FIV is a very similar genetically to HIV but they are not the same viral
species due to their relationship with different organisms (cats vs. humans)
viral species names do not follow binomial nomenclature and are in English

step 1: nucleic acid classification

will split into DNA or RNA viruses
from there, number and type of strands can be evaluated
DNA can be single-stranded or double-stranded
RNA can be single stranded, positive sense, negative sense or doublestranded

RNA vs. DNA viruses

a positive sense RNA can act like mRNA in
the cell and be directly translated
negative sense RNA must make a
complementary RNA strand before it can
be translated into proteins
Important RNA viruses include:
Picornavidae family (naked, positive
sense, include poliovirus, hepatitis A,
and rhinovirus)
retroviridae (enveloped, 2 positive
sense strand RNA. They use reverse
transcriptase to make the RNA turn
into DNA before it was utilized. HIV is
an example.)
Orthomyxoviridae (enveloped,
negative sense RNA. Influenza is an

most are double stranded and families
separated based on shape of the DNA
(linear or circular), capsid shape and
presence of an envelope
Herpesviridae (enveloped, linear dsDNA
viruses. Large family of animal viruses
that always includes a latancy period,
such as chickenpox into shingles. HSV1,
HSV2, and Epstein-Barr are also in this
Poxviridae (enveloped, linear dsDNA and
include small pox)
Papovaviridae (naked, polyhedral viruses
that replicate in the nuclei of host cells,
such as HPV)

emerging viruses
viruses have been in the human population as long as there have
been humans
emerging viruses are those that were present in very low levels but due to
human movement and population density and are increasing or
were able to cross the species barrier and infect humans
ex: influenza
when more than one strain of influenza is present in a host, they can swap part of their
genomes which can result in an increase in their ability to infect a wider range of hosts,
increase their pathogenicity, or increase the severity of the disease

ex: swine flu

has pieces of pig flu and human flu in its genome

ex: avian flu

can jump from sick birds to humans and no genome jumping has been noted!
if it mixes with the human flu, it COULD start swapping human to human

viral replication cycles follow 5 general


attachment of viruses to host cells


entry of viruses into host cells


creation of new viral components


assembly of viral components


departure of new virions from host cell

virus: infectious, once its inside a cell and is using the host cells machinery for its own purpose
virion: inert form, holds genetic information

attack animal hosts, but may also attack bacteria!
highly specific, allowing them to be used in phage therapy to treat diseases without
killing normal microbiota in the patient
turn to p. 288, look at figure 10.12
You can do phage counts by doing serial dilutions on a bacterial lawn and counting the
plaque-forming units.

replication of a virulent bacteriophage
replication of a temperate bacteriophage
replication of an enveloped dsDNA animal virus
replication of a + sense RNA virus: poliovirus
replication of a + sense RNA virus: HIV

How would you culture viruses in a lab?

Could you use agar?
chicken embryos could be used for some
today cell cultures are utilized (individual animal cells grown in media)
allows us to visualize the viral effect on cells (cytopathic effect)
Trained virologists can identify a virus based on cytopathic effect.

Can viruses cause cancer?

What do you think?
RNA retroviruses can translate their RNA into DNA which will then
cause repeated replication of cells which will lead to tumors
DNA tumor viruses have a cytopathic effect that is production of
uncontrollable cell division of infected cells
uncontrolled cell division leads to tumors

have you heard of Creutzfeldt-Jacob disease? kuro? bovine
spongiform encephalopathy (mad cow disease)?
neurological diseases that always end in death and are not caused by a living
organism or a virus but by a proteinacious infectious particle called a prion

prions have the following characteristics:

resistant to inactivation by heating to 90 C, which will inactivate viruses

not sensitive to radiation treatment
not destroyed by enzymes that digest DNA or RNA
sensitive to protein denaturing agents
have direct paring amino acids

a prion can induce other proteins in the brain to become prions,

eventually leading to the breakdown of neurons and cessation of
brain function. The only way to successfully eliminate prions is
incineration of body tissue.

Protist Characteristics
kingdom Protista
[mostly] unicellular, eukaroyotic organisms
while debate is ongoing, were going to focus on the two
plant-like (algae)
animal-like (protozoa)

mostly aquatic
diatoms: important producers in aquatic environments
dinoflagellates: second most important producers in marine environments
there are species within both groups that are capable of producing neurotoxins.
When these species bloom, heterotrophic organisms such as shellfish consume a large
number of these algae and the neurotoxins build up in the shellfish tissue
when humans eat the shellfish, they get a large dose of the toxin, resulting in shellfish
dolphins may also die

large and diverse group but we will focus on parasitic protozoa
mastigophorans have flagella and include Trypanosoma (African Sleeping
Sickness), Leishmania (responsible skin lesions), Giardia (responsible for
diarrhea) and Trichomonas (responsible for vaginal infections).
Apicomplexans are immobile and include malaria (very complicated life cycle)
Amoebozoa move by pseudopods,
several species that cause diarrhea

diverse group of heterotrophic organisms that can be unicellular
(yeast)or multicellular (mold).
body of the fungus is called a thallus which consists of mycelium, a
loosely organized structure of threadlike hyphae.
The cell wall contains chitin, a polysaccharide.
can reproduce both sexually and asexually, often switching between
them generation

highly important
decomposers, produce antibiotics and can be parasitic
parasitic fungi have three requirements to be successful
proximity to host
ability to penetrate the host
and ability to digest and absorb nutrients from host cell
parasitic fungi often kill the cell so they can decompose it
human fungal diseases (mycoses) can be classified as superficial, subcutaneous, systemic
or opportunistic.

affect only keratinized tissue in skin, hair and nails (athletes foot)

affect skin layer beneath keratinized tissue to the lymph vessels (Candida
yeast infection)

involve internal organs (lung infection Histoplasmosis)

caused by fungi that only causes disease when host is already weakened
(fungal pneumonia in an AIDS patient)

fungi classification according to sexual

stage of life cycle
Zygomycota: bread molds that form multinucleaated zygotes during
sexual reproduction (Rhizopus is an opportunistic bread mold)
Ascomycota: sac fungi, diverse group including yeast, they produce
saclike ascus during sexual stage (includes most of the fungi of
importance to microbiology including Penicillium, Saccharomyces,
Candida albicans and Histoplasma)
Basidomycota: club fungi, include mushrooms, toadstools and other
multicellular fungi

parasitic worms
flatworms are primitive worms with simple digestive tracts
(roundworms, nematodes, flukes and tapeworms)
roundworms and nematodes have a primitive body cavity separating
their digestive system
most are hermaphroditic
includes earthworms
we will look at flukes, tapeworms, adult roundworms and roundworm

turn to pp. 328-331 in your books