Exam 3 Flashcards
dichotomous key
a series of yes/no questions that successively narrows down the possible categories of species
- most traits are phenotypic, such as cell size and motility
rapid pathogen identification
multiple color tests
- results scored to give most probable species
random mutations
occur as the chromosome replicates
reductive (degenerative) evolution
loss or mutation of DNA encoding unselected traits
organisms diverge from one another through several fundamental mechanisms: (3)
- random mutations
- natural selection and adaptation
- reductive (degenerative) evolution
molecular clock
temporal information contained in a macromolecular sequence
- based on the acquisition of new random mutations in each round of DNA replication
genes show that most consistent measures of evolutionary time encode components of the _____ and _____ apparatus
transcription, translation
which components of transcription/translation are a consistent measure of evolutionary time? (3)
ribosomal RNA and proteins, tRNA, and RNA polymerase
the most widely used molecular clock is the gene that encodes….
small subunit rRNA (SSU rRNA)
- 16s rRNA in bacteria
- 18s rRNA in eukaryotes
use of a molecular clock requires…
the alignment of homologous sequences in divergent species or strains
the frequency of differences between homologous sequences can be used to generate a _____ _____
phylogenetic tree
what do phylogenetic trees show?
estimates the relative amounts of evolutionary divergence between sequences of DNA
- can be used to infer the length of time since two species shared a common ancestor
symbiosis
microbes interacting with other organisms
mutualism
symbiosis that benefits both partners
parasitism
symbiosis that only benefits one partner, the other is harmed
commensalism
symbiosis that benefits one partner while the other is unaffected
rhizobium
mutalist bacteria that helps plants grow and absorb nutrients; fixes nitrogen in roots of plants
alphaproteobacteria
nitrogen-fixing bacteria
- rhizobium
gammaproteobacteria (4)
Name the bacteria.
- Enterics - E. Coli and relatives
- Vibrios and relative
- Pseudomonas - p. Aeruginosa
- Legionella
Gram negative, catalase positive, oxidase negative, rod-shaped facultative anaerobes which are bile-salt tolerant and often inhabit the gastrointestinal tract
gammaproteobacteria: vibrionales (3)
found in coastal water
- Vibrio cholerae causes cholera
- V. parahaemolyticus causes gastroenteritis
epsilon proteobacteria (3)
smallest group of proteobacteria
- Campylobacter causes diarrhea
- Helicobacter pylori: cause of stomach ulcers, stomach cancer
Barry Marshall and Robin Warren
awarded the Nobel Prize for their discovery that peptic ulcer disease was primarily caused by Helicobacter pylori
Chlamydia (3)
obligate intracellular parasites
- Trachomatis: causes STD and conjunctivitis
- Psittaci: causes psittacosis (parrot fever)
- Pneumoniae: causes and atypical pneumonia
chlamydia life cycle characteristics (3)
elementary body: non growing ‘spore-like’
reticulate body: vegetative cell
given up much metabolism: can’t make ATP
spirochaetes (3)
- spiral organisms with a sheath and axial filaments
- slow growing, aquatic free-living or parasitic
- several human pathogens
spirochaetes: human pathogens (2)
- Treponema pallidum: syphilis
- Borrelia burgdorferi: lyme disease
Firmicutes
low GC, gram-positive rods and cocci
Bacillales
aerobic or facultative anaerobes
bacillus (5)
endospore-forming rods; obligate aerobes; grow in soil
- B. subtilis: gram-positive model system
- B. anthracis: anthrax
includes extremophiles
listeria (2)
non-spore forming rods
- L. monocytogenes: enteric intracellular pathogen
staphylococcus (3)
non-spore forming cocci; hexagonal clusters
- S. aureus: toxic shock and lethal flesh infections
Clostridiales
anaerobic rods
clostridium (2)
what do they form?
what known disease do they cause?
forms endospores
- C. botulinum and C. difficile: tetanus
streptococcus (4)
non-spore forming cocci; chains
- Human throat flora
- group A streptococci causes strep and scarlet fever
Mollicutes
what do they lack? require?
what do they cause?
lacks cell wall and s-layer
requires animal host
- Mycoplasma genitalium: smallest known genome
- M. pneumoniae: causes pneumonia
firmicutes and actinobacteria (3)
- gram-positive
- peptidoglycan multiple layers; cross-linked by teichoic acids
- aerobes and facultative anaerobes
actinomycetes (3)
filamentous, producing aerial hyphae and spores
- Streptomyces: produce many antibiotics
- S. coelicolor, S. griseus
corynebacteriaceae
irregular rods
- Corynebacterium diphtheriae: diphtheria
mycobacteriaceae
exceptionally thick cell envelope holds acid-fast stain
- Mycobacterium
- M. tuberculosis: tuberculosis
- M. leprae: leprosy
proteobacteria and nitrospirae (4)
- gram-negative
- outer membrane contains LPS
- diverse metabolism
- lineage includes mitochondria
rhizobiales (3)
What kind of microbes are these?
plant mutualists and pathogens, methyl oxidizers, and animal pathogens
agrobacterium
A. tumefaciens: causes plant tumors; trasngenic plant vector
rhizobium (2)
related to agrobacterium, rhizobium, bradyrhizobium, sinorhizobium
- fix nitrogen intracellularly in legumes
rickettsia (4)
what does their lineage include?
includes intracellular parasites; lineage includes mitochondria
- R. rickettsii: rocky mountain spotted fever
- R. prowazekii: typhus
SAR11 cluster (2)
marine photoheterotrophs uses proteorhodopsin
- Pelagibacter
microbes are ubiquitous (2)
- in every habitable environment
- fill every potential niche
what can microbes use as a source of carbon or energy?
every component or product of a living cell
what determines a microbe’s ability to fill a niche? (2)
genome and environment factors
microbe producers (3)
algae, bacteria, phytoplankton
microbe consumers (3)
bacteria, archaea, eukaryotes
microbe decomposers (2)
fungi, viruses
environmental factors that determine microbial growth (5)
- oxygen levels
- availability of other nutrients
- temperature
- salinity
- pH
mutualistic microbes (3)
name three types
lichens: fungus + alga/cyanobacterium
rhizobium: inside leguminous plants
mixotricha: bacterial endosymbionts + termites
synergism
bother benefit through growth, but the partners are easily separated and they can grow independently of one another
amensalism
one species benefits by harming another; relationship is nonspecific
subdivisions of the environment surrounding roots (2)
- rhizoplane
- rhizosphere
rhizoplane
plant root surface
rhizosphere
region of soil outside the rhizoplane that receives substances from the roots
rhizobium-legume mutualistic interaction (4)
- legumes secrete flavonoid attractants
- rhizobium enters cortical cells where they differentiate into bacteroides with no cell wall
- bacteroides remain in symbiosome
- plant supplies catabolites, bacterium supplies fixed nitrogen, plant leghemoglobin sequesters excess O2
agrobacterium tumefaciens
- an alpha-proteobacterium
- causes crown gall disease
how does agrobacterium tumefaciens infect its host?
through a wound
how does agrobacterium tumefaciens affect its host?
T DNA transferred from bacterium to plant directs the host to overproduce phytohormones that cause tumor production, and to produce opines that attract more A. tumefaciens
where are the genes for infection and virulence encoded for in agrobacterium tumefaciens?
Ti, tumor inducing, plasmid
where is the carbon cycle’s major reservoir?
the ocean, atmospheric reservoir is MUCH smaller
aerobic carbon cycling (3)
- photosynthesis fixes CO2 into biomass, producing O2 and organic carbon compounds
- lithotrophs also reduce CO2 to biomass
- respiration returns CO2 to the atmosphere with a net gain of O2 and loss of CO2 in the photic zone
hydrologic cycle
- water flowing over ground picks up nutrients
- carbon and nitrogen runoff allows respiration
- respiring microbes deplete O2 in water
- BOD: biochemical oxygen demand - high BOD —> hypoxic costs —> fish die
the nitrogen triangle
both reduced and oxidized N is used for biomass
the nitrogen cycle (6)
- microorganisms decompose proteins from dead cells and release amino acids
- ammonia is liberated by microbial ammonification of the amino acids
- the nitrogen in ammonia is oxidized to produce nitrates for energy by nitrifying bacteria
- denitrifying bacteria reduce the nitrogen in nitrates to molecular nitrogen
- N2 is converted to ammonia by nitrogen-fixing bacteria
- ammonium and nitrate are used by bacteria and plants to synthesize amino acids that are assembled into proteins
nitrogen cycle:
proteins and waste products —(?)—> amino acids
what is this process called?
microbial decomposition
nitrogen cycle:
amino acids —(?)—> ammonia
What is this called?
microbial ammonification
nitrogen cycle:
ammonium ion —(?)—> nitrite ion
nitrosomonas, nitrification
nitrogen cycle:
nitrite ion —(?)—> nitrate ion
nitrobacter, nitrification
nitrogen cycle:
nitrate ion —(?)—> N2
pseudomonas, denitrification
nitrogen cycle:
N2 —(?)—> ammonia
nitrogen-fixation
sulfur triangle
sulfur cycle (3)
- SH2 is oxidized by anaerobic respirers to sulfate, removing toxic gas
- others reduce S into SH2
- algae excrete dimethyl sulfide, adding to atmospheric S
sulfur cycle:
proteins and waste –(?)–> amino acids
microbial decomposition
sulfur cycle:
amino acids (-SH) –(?)–> H2S
microbial dissimilation
sulfur cycle:
H2S –(?)–> SO4^2-
thiobacillus, for energy
sulfur cycle:
SO4^2- –(?)–> amino acids
microbial and plant assimilation