Exam 4 Flashcards
An organism’s phylogeny describes what?
A. acquisition of genes by horizontal gene transfer
B. genomic G+C content
C. chemical composition (percentage of C, N, P, etc.)
D. codon usage compared to other organisms
E. genetic relatedness to other species
E. genetic relatedness to other species
A(n) _____ is a group of organisms that all share a common ancestor, not shared with any other organism outside of its group.
clade
Which of the following does not represent a mechanism of horizontal gene transfer among prokaryotes?
A. acquisition of transposable elements
B. transduction
C. transformation
D. conjugal transfer of plasmid DNA
E. binary fission
E. binary fission
Which of the following conditions would most strongly favor adaptive evolution in bacteria?
A. continuous exposure to antibiotics
B. growth in a nutrient-rich broth
C. growth at moderate temperatures and pH
D. nonobligatory commensal relationships
E. absence of predators or viruses
A. continuous exposure to antibiotics
Which of the following traits of bacterial cells differ significantly from the other domains of life?
A. nature of genetic code
B. phospholipids in membrane
C. peptidoglycan in cell envelope
D. type of RNA polymerase
E. translation elongation factors
F. DNA as genetic material
C. peptidoglycan in cell envelope
D. type of RNA polymerase
E. translation elongation factors
What takes place inside of cyanobacterial carboxysomes?
A. buoyancy regulation
B. Krebs cycle
C. nitrogen fixation
D. carbon fixation
E. light-reactions of photosynthesis
D. carbon fixation
The two major genera of Gram-positive bacteria include the _______________ , which contains the endospore-forming genera (e.g., Bacillus and Clostridium), and the _______________, which contains some filamentous forms (e.g., Streptomyces) that produce exospores.
A. low GC Actinobacteria ; high GC Firmicutes
B. high GC Actinobacteria ; low GC Firmicutes
C. high GC Firmicutes ; low GC Actinobacteria
D. low GC Firmicutes ; high GC Actinobacteria
D. low GC Firmicutes ; high GC Actinobacteria
Nitrosomas spp. are betaproteobacteria which mediate which important step in the nitrogen cycle?
A. ammonia oxidation
B. ammonification
C. nitrate reduction
D. denitrification
E. nitrite oxidation
A. ammonia oxidation
The cyanobacteria are thought to have given rise to which eukaryotic organelle?
A. Lysosomes
B. The nucleus
C. Chloroplasts
D. Mitochondria
C. Chloroplasts
A Gram-positive bacterium with a low GC content may be a(n)
A. Nitrospirae.
B. Actinobacteria.
C. Firmicute.
D. Proteobacteria.
C. Firmicute.
An example of a Gram-positive, anaerobic, spore-forming microbe is
A. Anabaena.
B. Salmonella.
C. Clostridium.
D. Lactobacillus.
C. Clostridium.
The closest relatives of mitochondria are found in which bacteria class?
A. Gammaproteobacteria
B. Betaproteobacteria
C. Deltaproteobacteria
D. Alphaproteobacteria
D. Alphaproteobacteria
Bacteria used in wastewater treatment include those that can convert ammonia and nitrite to nitrate, decreasing the reduced nitrogen content of the sewage. These bacteria, such as Nitrosomonas spp., often belong in
A. Deltaproteobacteria.
B. Gammaproteobacteria.
C. Alphaproteobacteria.
D. Betaproteobacteria.
D. Betaproteobacteria.
The process of methanogenesis uses a series of specific cofactors to carry each carbon from CO2 (or another substrate) as it becomes progressively reduced by hydrogen. Which of the following is not a cofactor unique to methanogens?
A. coenzyme M (CoM)
B. methanofuran (MFR)
C. tetrahydromethanopterin (H4MPT)
D. cofactor F420 (F420)
E. flavin adenine dinucleotide (FAD+)
E. flavin adenine dinucleotide (FAD+)
With respect to O2 requirements, most methanogens are which of the following?
A. facultative anaerobes
B. strict aerobes
C. strict anaerobes
D. aerotolerant
C. strict anaerobes
Methanogenic bacteria are which of the following?
A. strict aerobes that obtain energy through the synthesis of methane
B. strict anaerobes that obtain energy through the consumption of methane
C. strict anaerobes that obtain energy through the synthesis of methane
D. strict aerobes that obtain energy through the consumption of methane
C. strict anaerobes that obtain energy through the synthesis of methane
Which of the following is true of all archaeans discovered to date?
A. They are unable to synthesize proteins.
B. None of them are human pathogens.
C. They are extremophiles.
D. They are more closely related to bacteria than to eukaryotes.
B. None of them are human pathogens.
Which of the following produces mushroom fruiting bodies?
A. Basidiomycota
B. Zygomycota
C. Ascomycota
D. Chytridiomycota
A. Basidiomycota
One reason why fungi cannot perform phagocytosis of food particles is that they
A. do not encounter food particles in their environments.
B. do not need to, because they are photosynthetic.
C. are surrounded by a stiff cell wall.
D. lack necessary cytoskeletal components such as actin.
C. are surrounded by a stiff cell wall.
Which of the following structures is most likely to be a component of both chytrid zoospores and motile animal cells?
A. Flagella
B. Cilia
C. Pseudopods
D. Frustule
A. Flagella
Which of the following characteristics are typical of fungi?
A. Mycelium
B. Mixotroph
C. Chloroplasts
D. Cell wall
E. Multicellular
F. Unicellular
A. Mycelium
D. Cell wall
E. Multicellular
F. Unicellular
Methanogens usually require
A. acidic conditions.
B. methane as a substrate.
C. association with bacterial species.
D. high temperatures.
C. association with bacterial species.
Life on Earth relies on the production, consumption, and recycling of nutrients. The position that an organism occupies within a food web is referred to as its _____.
trophic level
What are three types of assimilatory processes?
Photosynthesis
Chemoautotrophy
Nitrogen fixation
What are three types of dissimilatory processes?
Decomposition
Nitrification
Aerobic respiration of organic compounds
Which of the following represent prokaryotic primary producers?
A. moss
B. seaweed
C. viruses
D. protists
E. lithoautotrophs
F. fungi
G. cyanobacteria
E. lithoautotrophs
G. cyanobacteria
What is the order of the food web starting from primary producer?
Primary producer
Grazers
Primary predator
Secondary predator
Decomposers
Which of the following symbionts may be found in lichens?
A. chemoautotroph
B. cyanobacterium
C. zooxanthella
D. alga
E. moss
F. fungus
B. cyanobacterium
D. alga
F. fungus
Fungi that invade plant cells in their roots but do establish a mutualistic relationship are
A. endomycorrhizae.
B. ectomycorrhizae.
C. opportunistic pathogens.
D. generalists in terms of their mutualistic relationships.
A. endomycorrhizae.
Soil food webs differ from marine food webs in that
A. oxygen is present throughout.
B. the role of bacteria is greater than in all trophic levels.
C. decomposition is much less important.
D. primary production is done mostly by plants.
D. primary production is done mostly by plants.
Suppose various legume plant parts are rubbed with a protein gel. Which plant part is most likely to test positive for nitrogenase?
A. Roots
B. Leaves
C. Stems
D. Flowers
A. Roots
Which of the following does NOT contribute to eutrophication?
A. Antibiotic runoff
B. Excessive nitrogen inputs
C. Organic pollutants
D. Algal blooms
A. Antibiotic runoff
An organism classified as a barophile is most likely to be found in which habitat?
A. Euphotic zone
B. Benthic zone
C. Epilimnion
D. Aerated horizon
B. Benthic zone
How do viruses contribute in the food web?
Decompose bacteria
Biochemical oxygen demand (BOD) is controlled by the concentration of
A. multicellular organisms.
B. benthic microorganisms.
C. heterotrophic microorganisms.
D. autotrophic microorganisms.
C. heterotrophic microorganisms.
Syntrophy means
A. coupled metabolic pathways in one organism to achieve negative ΔG.
B. two organisms eating at the same trophic level.
C. using two metabolic pathways simultaneously.
D. multiple organisms needed to complete a metabolic pathway with negative ΔG.
D. multiple organisms needed to complete a metabolic pathway with negative ΔG.
Lichens are an example of a mutualism between an alga and a(n)
A. animal.
B. bacterium.
C. fungus.
D. plant.
C. fungus.
The major primary producers in terrestrial ecosystems are
A. fungi.
B. cyanobacteria.
C. earthworms.
D. land plants.
D. land plants.
A single-celled eukaryote feeds on cyanobacteria (photoautotrophs). The cyanobacteria are considered
A. grazers.
B. decomposers.
C. predators.
D. primary producers.
D. primary producers.
An organism fixes nitrogen for the production of amino acids. This is an example of
A. assimilation.
B. habitat.
C. dissimilation.
D. predation.
A. assimilation.
Despite the fact that the Earth’s crust contains approximately 3,000 times more carbon than the oceans, the oceans are a more important carbon reservoir for most living things. Why is this?
A. The carbon in crustal rock cannot be fixed by living organisms.
B. The oceans serve as a carbon source but not a carbon sink.
C. Carbon cycles quickly between crustal rock and living things.
D. Carbon cycles quickly between the oceans and living things.
D. Carbon cycles quickly between the oceans and living things.
What is the ranking of nitrogenous compounds from least oxidized to most oxidized?
NH3
N2
NO2-
NO3-
What are the types of carbon reservoirs from smallest amount to largest amount of carbon?
Atmosphere
Fossil fuel
Ocean
Earth’s crust
Which reservoir cycles carbon least rapidly? Middle? Most?
Earth’s crust
Oceans
Atmosphere
What are some factors of aerobic carbon cycling?
Supports higher rates of biomass production
Occurs in the photic zone of the ocean
Includes photosynthetic fixation of CO2
What are some factors of anaerobic carbon cycling?
Includes fermentation
Favors incomplete breakdown of organic material
Includes respiration that uses nitrate, Fe3+, and sulfate as electron acceptors
What process takes CO2+H2O and converts it to CH2O?
Photosynthesis
What process takes CH2O and converts it to CO2+H2O?
Aerobic respiration
What process takes CH2O and converts it to alcohols and acids (H2+CO2)?
Fermentation
What process takes alcohols and acids (H2+CO2) and converts them to CH2O?
Anaerobic lithotrophy
______ is a fully reduced form of carbon that accumulates deep underground due to limiting ______.
Methane
O2
Which of the following statements is true about the relationship between the concentration of organic compounds in a body of water and its biochemical oxygen demand (BOD)?
A. As the concentration of organic compounds decreases, the BOD increases.
B. The concentration of organic compounds does not affect the BOD.
C. As the concentration of organic compounds increases, the BOD decreases.
D. As the concentration of organic compounds increases, so does the BOD.
D. As the concentration of organic compounds increases, so does the BOD.
Which of the following is the most direct cause of a rise in biochemical oxygen demand (BOD) in bodies of water?
A. respiration by heterotrophs
B. chemosynthesis by lithotrophs
C. methanogenesis by methanogens
D. photosynthesis by cyanobacteria
A. respiration by heterotrophs
The hydrologic and carbon cycles interact. Organic carbon-containing compounds in water act as fuel for __________ by aquatic organisms. This process uses __________ and if the process occurs at too great a rate, __________ dead zones occur in the body of water.
A. photosynthesis, carbon dioxide, oxygenated
B. respiration, oxygen, hypoxic
C. respiration, carbon dioxide, oxygenated
D. photosynthesis, oxygen, hypoxic
B. respiration, oxygen, hypoxic
What are the three steps in the “nitrogen triangle”? Place them in the order needed starting from N2.
Nitrogen fixation
Aerobic nitrification
Anaerobic denitrification
Which of the following processes of the nitrogen cycle is an aerobic process?
A. nitrogen fixation
B. nitrification
C. anammox reaction
D. denitrification
B. nitrification
Which of the following nitrogen cycle processes returns N2 to the atmosphere?
A. denitrification
B. nitrogen fixation
C. anammox reaction
D. nitrification
A. denitrification
C. anammox reaction
Which of the following is the most oxidized form of carbon?
A. Methane (CH4)
B. Methanol (CH3OH)
C. Formic acid (HCOOH)
D. Carbon dioxide (CO2)
D. Carbon dioxide (CO2)
In a wastewater treatment plant, microbes are used primarily during __________ treatment.
A. secondary
B. quaternary
C. primary
D. tertiary
A. secondary
The primary source and sink of nitrogen is
A. the ocean.
B. the atmosphere.
C. forests.
D. soil.
B. the atmosphere.
Nitrogen is often a limiting nutrient for plant growth because
A. human activities have reduced the nitrogen concentration in the environment.
B. plants cannot use the most abundant form of nitrogen (N2).
C. it is a small percentage of the atmosphere.
D. nitrogen is not transported into plant cells efficiently.
B. plants cannot use the most abundant form of nitrogen (N2).
Cellular nitrogen fixation
A. can occur in both prokaryotes and eukaryotes.
B. leads to the oxidation of nitrogen.
C. occurs in the absence of an enzyme.
D. requires a lot of energy.
D. requires a lot of energy.
Which of the following is a true statement about dissimilatory nitrate reduction?
A. It occurs mainly in the presence of oxygen gas (O2).
B. Nitrate acts as an electron donor.
C. It is not an important pathway in the biogeochemical nitrogen cycle.
D. It can lead to the production of N2 or ammonia.
D. It can lead to the production of N2 or ammonia.
Which of the following is the most oxidized form of nitrogen?
A. NO
B. NH3
C. NO2–
D. NO3–
D. NO3–
Define clade:
group of species that once shared a common ancestor
Define taxonomy:
description of life forms and their classification into groups
What is the order of taxonomy from largest to smallest?
class-order-family-genus-species
Define horizontal gene transfer:
transfer of one or more genes between unrelated species
Define vertical gene transfer:
linked to DNA replication and cell duration
WHOLE GENOME copied and passed to offspring
Define symbiosis:
association between two or more species
Define mutualism:
type of symbiosis
both partner benefit
Define endosymbiosis:
type of symbiosis
one partner lives inside the body of another
Define syntrophy:
type of symbiosis
2 or more partners depend on each other for the completion of their metabolism
Define co-evolution:
endosymbiotic relationship where both partners evolve together
involves reductive evolution of the endosymbiont
Define ecosystem:
habitat and the organisms living in it
Define assimilation:
part of ecosystem
primary producers
-CO2 fixation, N2 fixation, photosynthesis
Define dissimilation:
part of ecosystem
consumers and decomposers
-respiration, fermentation, heterotrophy
What are the 4 ocean layers?
Neuston
Euphotic zone
Aphotic zone
Benthos
What is the neuston?
top ocean layer
interface between water and air
What is the euphotic layer?
the “true” layer of the ocean
few meters below surface, light CAN penetrate
What is the aphotic layer?
second to bottom layer of the ocean
deeper layers of the ocean were light CANNOT penetrate
What is the benthos?
bottom layer of the ocean
ocean floor and sediment below
What are the 2 soil layers?
Top
Bottom
What is unique about the top layer of soil?
aerobic layer
What is unique about the bottom layer of soil?
anoxic layer
Define bacteroid:
rhizobium sheds its cell wall when inside the root cells of leguminous plants
Define reservoir:
part of the biosphere with significant amounts of an element
-C, N, S
Define a sink:
part of a reservoir
where the element returns to
Define a source:
part of a reservoir
for the element for organisms that use it
Define biochemical O2 demand (BOD):
need for oxygen in an ecosystem
increases in a water body when waterbody gets eutrophied
What type of water body has a high BOD?
eutrophic
What type of water body has a low BOD?
oligotrophic
What are the 3 mechanisms of divergence from common ancestors?
Random mutation
Natural selection (gene gain)
Reductive evolution (unwanted traits lost)
Which gene is most commonly used in phylogenetic trees? Why?
SSU rRNA
universal and sequence of nucleotides differs between species
What are the 3 domains of life?
Archaea (prokaryote)
Bacteria (prokaryote)
Eukaryotes
What’s the difference between prokaryotes and eukaryotes?
prokaryotes do not have a true nucleus, eukaryotes do have one
What do all domains of life share?
DNA
Similar cell architecture (cytoplasm surrounded by cell membrane)
Central dogma
Define the central dogma of microbiology:
genes –> transcription –> RNA –> translation –> proteins
What types of metabolism are NOT present in eukaryotes?
N2 fixation
Lithotrophy
Methanogenesis
What types of metabolism are common to ALL domains of life?
Respiration
Fermentation
What type of metabolism are unique to archaea? Why?
Methanogenesis
–> archaea are strict anaerobes
–> CO2 needed for carbons
–> methanofuran needed as electron carrier
–> product id CH4 (methane, most reduced form of C)
–> occurs in anoxic environments (no oxygen)
What is an example of an anoxic environment?
landfills. waste treatment plants, etc
What domain of life has no known pathogens?
archaea
What do bacteria and archaea have in common?
circular genome
no true nucleus and no nuclear membrane
What passes in horizontal gene transfer?
a piece of DNA with 1 or more genes
Between what does horizontal gene transfer occur?
unrelated species
How does horizontal gene transfer occur?
with a plasmid (virus related)
conjugation –> transformation –> transduction
Why does horizontal gene transfer occur?
increases chances of survival under the current conditions
meets conditional needs
What passes in vertical gene trasnfer?
the full genome
Between what does vertical gene trasnfer occur?
mother cell and an offspring
How does vertical gene transfer occur?
1 - replicate DNA
2 - cell divides
Where was the endosymbiotic origin of mitochondria?
alpha-proteobacteria
What genes are encoded on the mitochondria that are important for the survival of the host?
respiration
Where was the endosymbiotic origin of the chloroplast?
cyanobacteria
What genes are encoded on the chloroplast that are important for the survival of the host?
CO2 fixation (CO2 –> sugar)
photosynthesis
What are some characteristics that diversify cyanobacteria?
photosynthesis is oxygenic
fixes CO2 via Calvin Cycle
carboxysomes
marine types can fix N2 using N2ase
heterocysts
What are the three subclasses of bacterium?
cyanobacteria
gram positive
gram negative
What are the two subclasses of gram positive bacteria?
firmicutes
actinobacteria
What is an example of actinobacteria?
mycobacterium
What are the two subclasses of firmicutes?
spore former
non-spore former
What types of bacteria are spore formers?
bacillus
clostridium
What types of bacteria are non-spore formers?
staphylococcus
streptococcus
What is an example of gram negatives bacterium?
proteobacteria
What are the 4 subclasses of proteobacteria?
alpha-proteobacteria
beta-proteobacteria
gamma -proteobacteria
delta-proteobacteria
What types of bacteria are alpha-proteobacteria?
rhizobium
N2 fixation
legume plants
What types of bacteria are beta-proteobacteria?
nitrosomonas
nitrification
What types of bacteria are gamma-proteobacteria?
E-coli dentrification
What types of bacteria are delta-proteobacteria?
Sulfate-reducing bacteria
Where can methanogens be found?
termite gut
rumen
waste water treatment
Where are halophilic archaea found? Why?
salted foods
solar salterns
hypersaltern lakes
NOT THE OCEAN/SEA
requires high concentration of salt
What are 3 traits common to all filamentous funhi?
1 - have chitin in cell wall
2- absorptive nutrition
3- myceluin / hyphae
What is a trait common in all unicellular fungi like yeast (non-filamentous)?
budding reproduction
What are the 4 fungal phyla? What are examples of each?
chytridis myata –> anaerobic rumen fungi
zygo –> glomus endomyeo rrhizae
aseo –> morelol truffles
basidis –> mushrooms
Define assimilation
inorganic elements become a form that we can assimilate
inorganic to organic
Define dissimilation
organic forms of an element breaks down to inorganic forms of element
organic to inoganic
What are some examples of assimilation?
CO2 fixation
photosynthesis
N2 fixation
What are some examples of dissimulation?
respiration
fermentation
At what trophic state does assimilation occur?
primary producers
At what trophic state does dissimulation occur?
consumers and decomposers
What organisms have a mutualistic relationship with lichens?
algae and/or cyanobacteria
bacteria
What is the function of the mutualistic relationships with lichens and algae/cyanobacteria/fungi?
photosynthesis and CO2 fixation provides C to the partner (algae/cyanobacteria)
protect the system (fungi)
What organisms have a mutualistic relationship with the termite gut microbes?
termite and other microbes in the gut
bacteria and methanogen
What is the function of the mutualistic relationship between the termite gut and the termite+community in the gut?
provide wood (termite)
break down wood (community)
endosymiotic relationship
What is the function of the mutualistic relationship between the termite gut and bacteria+methanogens?
break down wood into simple sugars + CO2 + H2 (bacteria)
help keep H2 concentration down (methanogens)
syntrophic relationship
What organisms have a mutualistic relationship with mycorrhiza?
plant roots and fungi
What is the function of the mutualistic relationship between mycorrhiza and plantroots+fungi?
photosynthesis and CO2 fixation provide C to fungus (plant roots) ECTOMYCORRHIZAE
absorb nutrient from meter away (fungi) ENDOSYMBIOSIS
penetrates inside root cells, endomycorrhizae (fungi) ZYGOMYCOTA
What organisms have a mutualistic relationship with leguminous plants?
plant roots and rhizobium
What is the function of the mutualistic relationship between leguminous plants and plant roots+rhizobium?
photosynthesis and CO2 fixation to provide fixed C to rhizobium (plant roots)
bacterois wall fixes N2 and creates Nh# (rhizobium)
endosymbiosis relationship
What organisms have a mutualistic relationship with the rumen microbes?
cow + community in gut
bacteria/fungi + methanogen
What is the function of the mutualistic relationship between the rumen microbes and the cow+community / bacteria+fungi+methanogen?
eat plants (cow)
digest plants (community
ABOVE ARE ENDOSYMBIOTIC
break down complex plant fibers (bacteria+fungi)
help keep H2 concentration down (methanogen)
ABOVE ARE SYNTROPHY
What are the primary producers in the ocean?
algae and cyanobacteria
What are the primary producers in the soil?
green plants
What are the consumers in the ocean?
bacteria and archaea
What are the consumers in the soil?
protists and fungi
What are the decomposers of the ocean?
viruses
What are the decomposers of the ocean?
viruses
What are the decomposers of the soil?
bacteria and fungi
In which stage of waste water treatment are microbes involved?
secondary treatment
Which microbes are involved in wastewater treatment? What do they do?
aerobic heterotrophs –> aerobic respiration to convert the C load to an organic form like CO2
methanogens –> help keep the H2 concentration down
How do we inoculate wastewater treatment bacteria and why?
pump O2 to keep aerobes happy
in the form of flocs
Where is the LARGEST reservoir of carbon?
carbonate rock / earth crust
Where is the FASTEST reservoir to recycle carbon?
atmosphere
Where is the LARGEST reservoir for nitrogen?
atmosphere
Eutrophic (true growth) water bodies have ____ carbon content and _____ biological O2 demand.
high, high
Oligotrophic (few) water bodies have _____ carbon content and _____ biological O2 demand.
low, low
What is the most negative oxidation state of carbon?
CH4
What is the most negative oxidation state of nitrogen?
NH3
What is the most negative oxidation state of sulfur?
H2S
What is the most neutral oxidation state of carbon?
organic C like sugar
What is the most neutral oxidation state of carbon?
N2
What is the most neutral oxidation state of sulfur?
elemental S
What is the most positive oxidation state of carbon?
CO2
What is the most positive oxidation state of nitrogen?
NO3 (nitrate)
What is the most positive oxidation state of sulfur?
SO4 (sulfate)
Most negative oxidation state means what?
lots of electrons
most REDUCED
can only be OXIDIZED
can only DONATE electrons
can only be an electron DONOR
Most positive oxidation state means what?
most OXIDIZED
can only be REDUCED
can only ACCEPT electrons
can only be an electron ACCEPTOR
Which element has the MOST oxidized state?
nitrogen
