—Taxonomy is defined as the science of biological classification
—Nomenclature deals with the assignment of names
Binomial system- established by Linnaeus, two names given to organisms- genus
and species
Archaea
Phylum Crenarchaeota
—Depend on sulfur for growth
—Are frequently acidophiles
Phylum Euryarchaeota
—Methanogens- obligated anaerobes that can obtain energy by making
(synthesizing) methane
—Halobacteria- aerobic chemoheterotrophs that require salt (NaCl 1.5M)
for growth. Found in salt lakes, salterns and salted fish
—Thermoplasms- lack cell walls and can live in hot acidic coal refuse piles.
—Extremely thermophilic sulfur reducers- live in hot environments and
can reduce sulfur to sulfide (S0 to S-2)
Sulfate-reducing archaea- extreme thermophiles
Bacteria
—Aquificae and Thermotogae- oldest phylogenetic branch of Bacteria. Are
hyperthermophilic gram-negative rods.
—Deinococcus- extremely resistant to desiccation and radiation. Include aerobic
cocci and rods.
Deinococcus radiodurans, nicknamed Conan the Bacterium, can withstand
1.5 million rads. Its extrordinary tolerance makes it useful at nuclear
waste sites, where it consumes nuclear waste and transforms it into more
disposable derivatives. Can withstand dehydration. Found in North Pole.
May have come from Mars.
Phylum Cyanobacteria- require oxygen to carry out photosynthesis. Many
Are nitrogen fixing bacteria for plants
•Phylum Chlamydiae- non-motile- coccoid, gram negative bacteria that lack
peptidoglycan and must reproduce within the cytoplasmic vacuoles of host
cells.
–Chlamydial infections include inclusion conjunctivitis, chlamydia
pneumonia, gonococcal urethritis, lymphogranuloma venereum, and
trachoma.
Phylum Spirochaetes- slender, long, helical, gram-negative bacteria that are
motile
- can cause Syphilis and Lyme disease
Phylum Proteobacteria – largest group of bacteria with over 500 known genera.
Class Alpha-Proteobacteria
Rickettsias- obligate intracellular parasites responsible for many
diseases including typhus, Rocky Mountain spotted fever, and
ehrlichiosis.
Ehrlichiosis is a bacterial illness transmitted by ticks that
causes flu-like symptoms.
Class Beta-Proteobacteria
Genus Neisseria contain non-motile, aerobic, gram-negative
Cocci that colonize mucous membranes causing disease such
As meningitis and gonorrhea
Class Gamma-Proteobacteria- largest group of proteobacteria
•Purple sulfur bacteria are anaerobes and usually
photolithoautotrophs that oxidize hydrogen sulfide to sulfur
•Methylococcaceae are methylotrophs, which means that they use
methane, methanol and other reduced one carbon compounds as
their energy source.
•Pseudomonas contain straight or slightly curved, gram-negative,
aerobic rods that are motile by one or several polar flagella
–Can cause many diseases, and often spoil refrigerated food.
–Enterobacteriaceae also known as enteric bacteria are
gram-negative and include human pathogens such as,
Salmonella, Shigellas, and some strains of E. coli
Class Delta-Proteobacteria- important in recycling sulfur within ecosystem
Bdellovibrio attacks other gram-negative bacteria by colliding with
them, then creates holes in membrane and enters periplasmic
space.
Class Epsilon-Proteobacteria include disease causing;
–Campylobacter
–Helicobacter
Phylum Firmicutes
Class Clostridia- genera Clostridium causes botulism, tetanus, and gas
gangrene
Class Bacilli- includes Staphylococcus that produce enzymes and toxins,
and genera Lactobacillus used for the fermentation of some food and dairy
industry. Also include Listeria, which causes food poisoning, and
Streptococcus, Enterococcus, Lactococcus.
Phylum Actinomycetes
•Include the genera and species Corynebacterium diphtheriae which
causes diphteria
•Include the genera Micrococcus
—Include Mycobaterium tuberculosis, Mycobacterium bovis, and
Mycobacterium africanus all of which cause tuberculosis
—Mycobacterium leprae cause leprosy
—Streptomyces important in the making of the drug first used against
tuberculosis
The Virus
A virus is composed of a capsid made up of protein and inside either RNA or DNA
Viruses are classified based on whether they have DNA or RNA and whether is a double
strand or not. The difference in nucleic acid causes them to replicate using different
mechanisms.
Double stranded DNA viruses, for instance, require host cell polymerases found in the
nucleus of a host cell in order to replicate its genome. These are highly dependent of the
cell’s cycle.
Those that have RNA, double or single stranded, normally are able to replicate in the
cytoplasm because they do not require the polymerases.
They are not dependent upon the cell’s cycle.
These viruses are usually fast replicating and cause lysis of the host immediately.
Define the following terms:
•Capsid- ___________________________________________________________________________
•Enveloped virus- _______________________________________________________________
•Induction- and event in the life in the life cycle of some viruses that results in the
provirus initiating synthesis of mature virions and entering the lytic cycle.
•Lytic cycle- ______________________________________________________________________
•Lysogeny- the state in which a viral genome remains within a bacterial or archaeal cell
after infection and reproduces along with it rather than taking control of the host cell
and destroying it.
•Naked virus- virus lacking the envelope
*Provirus (prophage)- __________________________________________________________
•Retrovirus- a member of a group of viruses with RNA genomes that carry the enzyme
reverse transcriptase and from a DNA copy of their genome during their reproductive
cycle. Retroviruses are different in that they have RNA but use DNA as an intermediate.
These viruses stay in a lysogenic stage and are able to replicate as the host develops new
cells of its kind. Then as environmental conditions change, they can then enter a lytic
stage.
•Virulent viruses- ________________________________________________________________
Stages of Viral Multiplication
1. •_________________________(adsorption)- mediated by an interaction between
receptors on the surface of a cell and molecules (ligands) on the surface of the virion.
2. •_________________________- viral nucleic acid enters the cell
3. •Synthesis of viral proteins and nucleic acids
4. •_________________________- once the nucleic acid has been duplicated the new
capsids and nucleic acids join
5. •_________________________- released- lysis of cell
•Some DNA phages, which need the nucleus of their host cell, are also temperate phages.
•That is they lyse a small fraction of bacterial cell while the rest continues a lysogenic
stage.
•Lambda phages are an example of such.
•In the lysogenic stage the viral chromosome becomes integrated into the host
chromosome and is called a ___________________________.
•It behaves as a gene of the host and replicates along with the host chromosome and is
inherited the same as the bacterial genes.
•Some bacteria change when they have a lysogenic virus such as Vibrio cholerae, which
when infected with the phage CTX produces the cholera toxin.