Microbiology - EXAM 3 (study guide)

classification

putting organisms into groups of relatedness

taxonomy

system of groups

systematics

science of determining the systems of groups

what is Bergey’s Manual, why?

considered the bible of the microbial taxonomy, classifies each organisms in the more current taxonomic system

• uses both phenetic and genetic criteria for classification and defines genus and species

what are the 5 kingdoms

plants, animals, fungi, protozoans, and monera

why are the kingdom trees obsolete

the first four are eukarya with one domain of life, monera include the bacteria and the archea (other two domains of life)

vertical gene transfer

parent to child, heredity

horizontal gene transfer

within the generation often between species, if the gene being used to follow a lineage is passed horizontally, we will get the wrong answers

why are SSU rRNA gene sequences used to make the current tree of life

16S and 18S rRNA gene sequences are highly conserved and key for an indespensible process, protein synthesis.

• not transfered horizontally, have universal conserved regions and hyper variable regions

what are the three domains of life

eukarya, bacteria, archea

what process are gene sequences compared to make phylogenetic trees

rRNA sequences are aligned that each base position is lined up between the sequences being compared, clustalW is the classic program

structure of dendrograms, how it relates to relatedness

nodes show common ancestors, the lengths are evolutionary time as determined by a model of the rate of different types of mutations

defining characteristics of viruses

acellular organisms, obligate parasites and must be inside of cells to reproduce, that are classified by their shape and genome types

what are viruses composed of

nucleic acid (dsDNA, ssDNA, dsRNA, or ssRNA) and proteins. enveloped viruses also have a lipid bilayer made of host cell lipids

what is a capsid, what is it made of

protein coat of the virus surrounding the genome

what is a protomer

protein subunit of the capsid (capsomer)

what is a viral envelope and what is it made from

host cell lipids, the bilayer is formed when the virus buds out of the cell

what are spikes and what is their role

integuments that are proteins which stick out of the viral capside, often for adhesion to cells by binding to cell surface protein receptors, some have enzymatic activity that help binding penetration or release of virions

what are the three main parts of bacteriophage

head where the genome resides, shaft, and tail fibers

what can viral genomes be made from

dsDNA, ssDNA, dsRNA, ssRNA

how does ssRNA viral replication differe from dsRNA viral replication or dsDNA viral replication

ssRNA genomes need to have a complimentary strand made, in order to make more viral genomes, dsRNA already has two strands needed for replication

retrovirus, along with life cycle

RNA viruses that are copied into DNA by reverse transcriptase, viral genome integrates into the host cell chromosome at this point.

• lives as a lysogen, producing virus, maybe making cytotoxic factorss

steps of lytic cycle

attachment, penetration, synthesis, assembly, maturation

attachment

of the virion to the cell surface

penetration

viral genome into the host cell

synthesis

virus takes over the cell and makes more virus

assembly/maturation

the new virons are formes, lysis where the cells burst releasing the progeny virus

how do animal viruses penetrate cells

tend to be enveloped viruses, their lipid bilayer fuses with the plasma membrane of the host cell, where the capsid enters the cell and uncoats releasing the viral genome

key features of the lysogenic cycle

attachment, penetration, latent phase, viral genome can intergrate into the host cell and survive as a phagemid or the intact capside

• viruse can be induced to reactivate, goes through the rest of the lytic cycle

prophage/provirus

viral genome inserted into the hos cell chromosome

how are laten viruses induced

stress, like getting old or infirm, immunocompromised

transduction

movement of genes between cells mediated by viruses

generalized transduction

when the viral genome inserts randomly into the genome and pops back out taking random sequences with it

specialized transduction

happens at known sites in the genome and take known marker genes with it

prion

proteinaceous infectious particle, acellular pathogen that is not a virus, are mis-folded brain particles, Mad Cow Disease

viroid

naked piece of mRNA that is infective and pathogenic, acellular pathogen that is not a virus, Citrus Canker

bacteria

are lipid bilayers which esterlinked lipids

archaea

cell membranes that are often etherlinked lipids and with areas of monolayers

• walls are pseudopeptidoglycan, include S-layer

• shares similarities with Eucarya, some are mathanogens and some have bacteriorhodopsin (photosynthesis)

what makes archaeal plasma membranes different than other cells

ether linked lipids, tertraethers, that span the membrane as a monolayer found in many archaea

• ether bods are more chemically stable than ester linked lipids

• archaea often tolerate to extreme environmental conditions

what is an S-layer

protein bag that protects the cell

light-harvesting cycle used by haloarchaea that contain bacteriorhodopsin

not like plant photosynthesis, involves no photosystems or electron transport chains

• membrane protein has a pigment that absorbs light and changes shape, that moves from inside to the outside carrying a protein

• builds up an H+ gradient for chemiosmosis

two major groups of protists

protozoans, algae

ectoplasm

perphery of the cytoplasm, firm in gel state and supports the cell shape

endoplasm

towards the center of the cell, more fluid, in a sol shape

pellicle of protozoans

set of protein bands that give the cell shape

protozoan cysts

tough reproductive cells

modes of motility for protozoan

flagella, cilia, amoeboid movement

holozoic

eating whole food particles

saprozoic

releasing enzymes to break down big food molecules and ingesting the small soluble molecules

schizogony

during reproduction when one cell gives birth to many small cells, usually infective particles

major groups of protozoans

zooflagellates, cilliates, apricomplexa

apical complex

area at the tip of the cell where organelles are concentrated (mitochondria)

micronucleus

reproduction

macronucleus

reduced gene set, used to control cellular metabolic activities

planktonic

float in water column

neustonic

live at the water-air interface

benthic

stuck to surfaces

frustule

silicon shell made by diatom algae

red tide

toxic algal bloom of dinoflagellates

crenarchaeota

hyperthermophiles (pH 2-3)

sulfolobus

makes elemental S granules and produce sulfuric acid with oxygen or iron as oxidant

thermoproteus

strict anaerobe using H2 and S0 with CO or CO2 as C source

mesophilic crens

widespread but understudied

euryarchaeota

includes methanogens and halobacteria

• methanogens use CO2 as terminal electron acceptor and produce methane, old metabolism only found in archaea, anoxic sediments, methanofuran, CoM, F420 for C1 metabolism

euryachaeota, groups

methanobacterium, methanococcus, methanosacrina

halobacteria

halophiles, cells filled with compatible solutes to balance osmotic pressure, contains bacteriorhodopsin in purple membranes

halobacteria, groups

halobacterium salinarum, haloferax

other archaea groups

korarchaetoa, nanoarchaeota, thaumarchaeota

which organisms have branches deep in the tree close to the root

thermophilic chemolithoautotrophs

aquaficae

aquifex pyrophilus, deepest branching, hyperthermophile, H2 bacteria, chemolthoautotrophic

thermatoga

hyperthermophile, chemoheterotroph

deinococcus

mesophile, most resistant to radiation

deep branching bacteria

aquiface, thermatoga, deinococcus

alphaproteobacteria

G-, oligotrophs including methylotrophs (C1 organisms), chemolithotrophs (nitrification), N2 fixers (rhizobia

rickettsias/chlamydias

G-, oligate intercellular parasites with reduced genomes, non-motile, very small, no glycolysis, ATP-dependent

• escape phagosomes and reduce and burst cells

rickettsias

coxiella, ehrlichia, bartonella

coxiella

Q fever

ehrlichia

fatal blood disease

bartonella

cat scratch fever

rickettsia typhi

typhus and R. rickettsii causes Rocky Mountain Spotted Fever

chlamydias

chlamydia trachomatis, C. psittaci, C. pneumoniae

• make reticulate bodies in phagosomes and release elemental bodies to spread

chlamydia trachmatis

leading cause of blindness by disease (trachoma) and STD

C. psittaci

parrot fever

C. pnemoniae

mild

brucella

brucellosis, obligate parasite, undulant fever

caulobacteriaceae/hyphomicrobiaceae

stalked bacteria, form prostheca (hyphae), stalk (holdfast), and budding reproduction (hyphae with buds)

• unusual life cycle, oligotroph with C1 metabolism

rhizobium

nitrogen-fixers that form nodules on plant roots

• in nodules, lose most genes and become bacteroids, accumulate PHB

rhizobium, bacteria

azotobacter, bradyrhizobium, agrobacterium (tumors and gene transfer in plants

alphaproteobacteria

rickettsids/chylamydias, bartonella, ehrilichia, coxrella

betaproteobacteria

eutrophs (copiotrophs) in organic-rich areas, between aerobic/anaerobic areas

neisseria

N. gonorrhoeae, N. meningitidis

N. gonorrhoeae

STD

N. meningitidis

epidemic meninggococcal meningitis

burkholderiales

formerly apart of Pseudomonas, very diverse, G-, aerobic nonfermetative, mesophilic, motile, PHB, tend to degrade xenobiotics

burkholderiales, bacteria

B. cepacia, Alaligenes, Leptothrix (forms sheaths, Fe, Mn metabolism), bordetella pertussis, whooping cough

hydrogenophilates

thiobacillus, S0 oxidation to sulfuric acid by odd pathway, lithoautotroph, acid mine drainage

gammaproteobacteria

very diverse group of G-

thiotrichales

beggiatoa, oxidize S0 to sulfate in sediments

methylococcus

methylomonas, oxidize methan to methanol and formaldehyde to run electron transport chain