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Bio 12 Exam 2
Bacteria, Archaea, Invertebrae, and Plants
154
Biology
Undergraduate 1
03/22/2011

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Term
5 Characteristics of Prokaryotes
Definition

1) Generally single-celled organisms

2) Greatly outnumber and outweigh all eukaryotes

3) Flourish in all habitats

4)Usually 0.5-5 micrometersin diameter

5) Usually spheres (cocci), rods (bacilli), or spirals (spirullus)

Term
Peptidoglycan
Definition

A matrix composed of modified-sugar polymers cross-linked by short polypeptides

- Found in the cell walls of bacteria but NOT archaea

Term
Gram Stain
Definition
An important tool for identifying bacteria
Term
Gram-positive
Definition

Bacteria with walls containing a thicker layer of peptidoglycan

- Appears blue or violet

Term
Gram-negative
Definition

Bacteria with more complex walls including an outer lipopolysaccharide membrane

- Appears red

Term
Capsule
Definition
Sticky secretion of prokaryotes outside the cell wall that serves as protection from attack by a host's immune system and as glue for adhering to a substrate or other prokaryotes
Term
Fimbrae
Definition
Hairlike appendages on the outside of a prokaryote's cell wall
Term
Sex pili
Definition

Hairlike appendages on the outside of a prokaryote's cell wall that are specialized for the exchange of DNA between prokaryotes

-Longer and less numerous than fimbrae

Term
Prokaryotic flagella differ from eukaryotic flagella by...(3)
Definition

1) Lack of a plasma membrane cover

2) Structure

3) Function

Term
Taxis
Definition
An oriented movement in response to chemical, light, or other stimuli
Term
Nucleoid
Definition
Region containing the circular DNA chromosome
Term
Plasmids
Definition
Smaller rings of DNA that may carry a few genes
Term
Endospores
Definition
Tough-walled dormant cells produced by some bacteria that are formed in response to a lack of nutrients
Term
Transformation
Definition
A process where foreign DNA is integrated into the bacterial chromosome by an exchange of homologous DNA segments
Term
Transduction
Definition

A process where a random piece of host DNA may be accidentally packaged within a phage and introduced into a new bacterium

- Recombination may occur when the newly introduced DNA replaces the homologous region of a bacterial chromosome

Term
Conjugation
Definition
A bacterial cell temporarily joins to another cell by sex pili and the donor cell transfers DNA to the recipient through a "mating bridge"
Term
F factor
Definition
A special piece of DNA that is either part of the chromosome or a plasmid that causes the ability to form pili and donate DNA
Term
F plasmid/F+ cells
Definition
Bacterial cells containing the F factor
Term
Hfr Cells
Definition
"High frequency of recombination"; cells in which the F factor is inserted into the bacterial chromosome
Term
R plasmids
Definition
Plasmids that carry genes that code for various mechanisms of resistance to anitbiotics
Term
Photoautotrophs
Definition
Use light energy and CO2 to synthesize organic compounds
Term
Chemoatuotrophs NEED TO EDIT
Definition
Use inorganic substances and CO2 to synthesize organic compounds
Term
Photoheterotrophs NEED TO EDIT
Definition
Use light energy and carbon in organic form to produce organic compounds
Term
Chemoheterotrophs
Definition
Use organic molecules as both an energy and a carbon source
Term
Obligate aerobes
Definition
Need O2 for cellular respiration
Term
Facultative anaerobes
Definition
Can use O2 for cellular respiration but also can grow in anaerobic conditions using anaerobic respiration or fermentation
Term
Obligate anaerobes
Definition
Are poisoned by O2; some use anaerobic respiration to break down nutrients with inorganic molecules other than oxygen serving as the final electron acceptor
Term
Nitrogen Fixation
Definition
Some cyanobacteria and a few other prokaryotes obtain nitrogen by converting atmospheric N2 to ammonia
Term
Heterocytes
Definition
Cells that perform nitrogen fixation
Term
Biofilms
Definition
Surface-coating colonies characterized by intercellular signaling, proteins that adhere to cells to each other and to the substrate, and channels int eh colony for movement of nutrients and wastes
Term
Extremophiles
Definition

Species that live in extreme habitats

- Many archaea are extremophiles

Term
Extreme halophiles
Definition

Organisms that live in extremely saline waters

- Many halophiles are in the clade Euryarchaeota

Term
Extreme thermophiles
Definition

Organisms that live in hot sulfur springs and near deep-sea hydrothermal vents

- FIt into the clade Crenarchaeota

Term
Methanogens
Definition

Organisms that have a unique energy motabolism in which CO2 is used to oxidize H2, producing methane (CH4) as waste

- Methanogens live in swamps/marshes and are important decomposers in cattle and other herbivores

- In the clade Euryarchaeota

Term
5 Major Groups of Bacteria
Definition

1) Proteobacteria

2) Chlamydias

3) Spirochetes

4) Gram-positive Bacteria

5) Cyanobacteria

Term
Proteobacteria
Definition

A nutritionally diverse group of aerobic and anaerobic gram-negative bacteria

- 5 Subgroups of Proteobacteria

1) Alpha proteobacteria: many are mutually symbionts or parasites of eukaryotes

2) Beta Proteobacteria: including soil bacteria Nitrosomonas

3) Gamma Proteobacteria: including photosynthetic sulfur bacteria and pathogens and enterics like E. coli

4) Delta Proteobacteria: including the colony-forming myxobacteria

5) Epsilon Proteobacteria: the mostly pathogenic group including stomach ulcer-causing Heliobacter pylori

Term
Chylamydias
Definition
Obligate intracellular animal parasites that are gram-negative
Term
Spirochetes
Definition

Helical heerotrophs that move in a corkscrew fashion

- Cause syphilis and Lyme disease

Term
Gram-Positive Bacteria
Definition

A diverse group with subgroups

- Actinomycetes: most are colonial soil bacteria; responsible for anthrax and botulism

- Mycoplasmas: the smallest of all cells and the only bacteria that lack cell walls

Term
Cyanobacteria
Definition

Have plantlike, oxygenic photosynthesis and are important producers in freshwater and marine ecosystems.

-Some filmanetous cyanobacteria have specialized cells for nitrogen fixation

Term
Decomposers
Definition

Organisms that return carbon, nitrogen, and other elements to the environment for assimilation into new living forms

- Decomposers convert inorganic compounds into forms that other organisms can use

Term
Symbiosis
Definition

An ecological relationship involving closer contact between organisms of different species

- Host (larger organism) and symbiont (smaller organism)

Term
Mutualism
Definition
Both species benefit (+/+)
Term
Commensalism
Definition
One organism benefits while the other is neither harmed nor helped (+/0)
Term
Parasitism
Definition
A parasite eats portions of the host (+/-)
Term
Pathogens
Definition
Parasites that cause disease
Term
About one half of all human disease are caused by...
Definition
...pathogenic prokaryotes which produce toxins
Term
Exotoxins
Definition
Proteins secreted by prokaryotes that cause such disease as botulism and cholera
Term
Endotoxins
Definition

Lipopolysaccharides released from the outer membrane of gram-negative bacteria that have died

- Cause typhoid fever and Salmonella food poisoning

Term
Bioremediation
Definition

The use of organisms to remove environmental pollutants

- Used to treat sewage, oil spills, mining industry, etc.

Term
Protists
Definition

Eukaryotes that are not fungi, plants, or animals

- Primarily unicellular organisms but include a few multicellular species

Term
Mixotrophs
Definition
Both photosynthetic and heterotrophic
Term
All eukaryotes have _____ or signs of having had them, as it evolved from _____ within the earliest eukaryotes
Definition
mitochondria, endosymbiotic alpha proteobacteria
Term
Plastids evolved from _______ that became an endosymbiont of a heterotrophic eukaryote
Definition
photosynthetic cyanobacterium
Term
Secondary endosymbiosis
Definition
A red or green alga was engulfed by a heterotrophic eukaryote, leading to a new protist lineage
Term
5 Supergroups of Eukaryotes
Definition

1) Excavata

2) Chromalveolata

3) Rhizaria

4) Archaeplastida

5) Unikonta

Term
Excavata
Definition

Based on morphological studies of the cytoskeleton and an "excavated" feeding groove found in its members

- Include protists with modified mitochondria and protists with unique flagella

Term
Diplomonads
Definition

Have two nuclei, modified mitochondria, no plastids, and multiple flagella

- Have mitosomes which have an undetermined function and lack electron transport chains

Term
Parabasalids
Definition

Flagellate protozoa, whose flagella are arranged in clusters near the anterior of the cell.

- Anaerobic

- Contain reduced mitochondria called hydrogenosomes which generate energy anaerobically, releasing H2

Term
Euglenozoans
Definition
A diverse clade containing predatory heterotrophs, autotrophs, and pathogenic parasites which all have a spiral or crystalline rod inside their flagella
Term
Kinetoplast
Definition

A single large mitochondrion containing a mass of DNA

-Characteristic of the group kinetoplastids which include free-living heterotrophs and parasites

Term
Euglenids
Definition

Characterized by one or two flagella that emerge from the anterior end

-Many photosynthetic Euglena switch to heterotrophy in the absence of sunlight

Term
Chromalveolata
Definition
The large diverse clade proposed by DNA data and evidence that some originated by secondary endosymbiosis by engulfing a red alga
Term
Alveolates
Definition

A major line of protists characterized by membrane-bound alveoli under the plasma membrane

- Alveoli stabilize the cell surface or osmoregulate

- Include the phylas dinoflagellates, apicomplexans, and ciliates

Term
Dinoflagellates
Definition

Unicellular with two perpendicular flagella between cellulose plates that creates a spinning movement

- Make up a large proportion of marine and freshwater phytoplankton

- Half of dinoflagellates are hetertrophic

Term
spongocoel
Definition
the central cavity of sponges into which water is drawn through pores in the body wall
Term
osculum
Definition
the point of exit of water through the body of the sponge
Term
choanocytes
Definition

collared, flagellated cells that line the spongocoel and help in collecting food partilces

*resemble the cells of choanoflagellates

Term
mesohyl
Definition
gelatinous matrix between the two body wall layers of the sponge
Term
amoebocytes
Definition

cells in the mesohyl that take up food, digest it, and carry nutrients to other cells (in place of true tissue)

they also form skeletal fibers = spicules or fibers

Term
sponges
Definition

-sessile animals founds in fresh and marine waters

-hermaphrodites - sperm carried through osculum and fertilize eggs retained in neighboring sponge mesohyl

-produce defensive compounds

Term
cnidarians
Definition

hydras, jellies, anemones, corals

anatomy: sac with central gastrovascular cavity and single opening that serves as both mouth and anus

two forms: polyp + medusa

Term
polyp
Definition
sessile, cylindrical form of cnidaria with mouth and tentacles extending upwards
Term
medusa
Definition
flattened, mouth-down polyp that moves by passive drifting and weak body contractions (other form of cnidaria)
Term
cnidocytes
Definition
found on the tentacles of cnidarians. contain cnidae and nematocysts (stinging capsules)
Term
hydraozoans
Definition
alternate between asexual polyp and sexual medusa. common, freshwater hydras exist only as polyps
Term
scyphozoans
Definition
medusa stage is more prevalent - sessile polyp stage often doesn't occur in jellies in the open ocean
Term
cubozoans
Definition
box-shaped medusa stage and coplex eyes in the fringe of their medusae. many species have nighly toxic cnidocytes
Term
anthozoans
Definition
sea anemones and corals occur only as polyps. corals secrete calcified external skeletons and the accumulation of this produces coral
Term
clade bilateria
Definition
bilaterally symmetrical animals with tripoblastic development, most of which are coelomates: lophotrochozoa, ecdysozoa, deuterostomia
Term
lophotrochozoa
Definition

lophophore: feeding structure found in members and trohochophore larva in others

*phyla include: flatworms, turbellarians, trematodes, cestoidea, rotifers, 

Term
flatworms
Definition
marine, freshwater, and moist terrestrial animals. tripoblastic acoelomates. branching gastrovascular cavity - functions in both digestion and food distribution. gas exchange and diffusion of N2 waste occur across body wall 
Term

protonephridia

Definition
network of tubules in flatworms with ciliated flame bulbs that pull fluids out of the body and function in osmoregulation
Term
Turbellarians
Definition
freshwater planaria and free-living flatworms. planaria use cilia to glide/swim. eyespot on head detect light, and lateral head flaps detect chemicals. nervous system is a pair of anterior ganglia and ventral nerve cords. sexual and asexual reproduction
Term
Trematodes
Definition
parasites living in or on other animals: flukes have tough outer covering, suckers and extensive reproductive systems. 
Term
Cestoidea
Definition
tapeworms have a scolex, with suckers and hooks for attaching to host's intestinal lining, plus proglottids packed with reproductive organs. predigested food is absorbed from the host
Term
Rotifers
Definition
alimentary canal with separate mouth and anus. fluid in the pseudocoelom functions as a hydrostatic skeleton and distributes nutrients. crown of cilia draw food into the mouth to the pharynx with "jaws". asexual reproduction through parthenogenesis, resulting resistant zygotes survive harsh conditions in a dormant state
Term
parthenogenesis
Definition
female offspring develop from unfertilized eggs
Term
lophophorates
Definition
ectoprocts and brachiopods: have lophophores, crown of ciliated tentacles, true coelom 
Term
ectoprocts (bryozoans)
Definition
tiny marine animals living in colonies with hard exoskeletons and pores through which lophophores extend
Term
brachiopods
Definition
attach to seafloor by stalk and open hinged shell to let water flow through lophophore
Term
molluscs
Definition
muscular foot (movement), visceral mass (internal organs), mantle (covers visceral mass and may secrete a shell). mantle cavity encloses gills, anus, and excretory pores. radula = feeding. nerve ring and nerve cords 
Term
chitons
Definition
oval marine animals with shells that are divided into 8 dorsal plates
Term
gastropods
Definition
distinctive feature = torsion, the embryonic rotation of the visceral mass that results in the anus and mantle cavity being above the head. distinct heads with eyes at the tips of tentalces
Term
bivalves
Definition
clams, oysters, mussels and scallops: two havles of shell hinged at mid-dorsal line. suspension feeders - water flows in and out of mantle cavity through siphons and food trapped in mucus
Term
cephalopods
Definition
rapid-moving carnivoers. mouth has beaklike jaws t bite prey. shell is reduced and internal in squids, absent in octopuses, and external in chamberd nautilus. foot modified to form parts of tentacles. only molluscs with closed circulatory system well developed nervous system, senses, and brain. 
Term
annelids
Definition
segmented worms: ogliochaetes, polychaetes, leeches
Term

oligochaetes

 

Definition
closed circulatory system - respiration occurs across moist, highly vascularized skin. septa separate coelom into segments (excretion), nervous system = cerebral ganglia +fused segmental ganglia along ventral nerve cord. all earthworms are hemaphrodites
Term
polychaetes
Definition
marine worms with parapodia on each segment that function in locomotion + gas exchange. planktonic, bottom burrowers, tube dwellers
Term
leeches
Definition
fresh water: feed on small invertebrates or slit/digest hole through skin to suck blood out of host
Term
ecdysozoans
Definition
animals that molt, shedding external cuticle: nematodes and arthropods
Term
nematodes
Definition

roundworms: water, soil, bodies of plants and animals. tough cuticle, alimentary canal. fluid in pseudocoelom circulates nutrients. reproduction is sexual, fertilization is external, zygotes are resistant cells.

*decomposers, pests, parasites

Term
arthropods (1)
Definition

segmentation, hard exoskeleton, joined appendages. 

evolved from lobopods - extant lobopods share all the arthropod Hox genes. 

exoskeleton probably first evoloved in seas as protection and muscle anchorage, but with terrestrial diversification, now functions as protection from desiccation support

Term
arthropods (2)
Definition

extensive cephalization and well-developed sensory organs. 

heart pumps hemolymph through open circulatory system (hemocoel)

tracheal systems of branching internal ducts (rather than gills in aquatic species)

4 lineages: cheliceriforms, myriapods, hexapods, crustaceans

Term
cheliceriforms 
Definition

horseshoe crabs, scorpions, spiders, mites, ticks

clawlike chelicerae = pincers/fangs for feeding

anterior cephalothorax and absomen

*arachnids: book lungs function in gas exchange

Term
myriapods
Definition
millipedes (vegetarians - 2 pairs of leg per segment): centipedes (carnivores - poison pincers, 1 pair of legs per segment)
Term
hexapods
Definition

insects: head has fused segments with antennae, compound eyes, mouthparts, thorax, abdomen with obvious segments.

nervous system: cerebral ganglion and paired ventral nerve cords with segmental ganglia. 

malpighian tubules, outpockets of digestive tract, function in excretion

trachael tubes - respiratory system

Term
crustaceans
Definition
two pairs of antennae; 3+ mouthpart appendages. larger ones have gills through which nitrogenous waste pass (through diffusion)
Term
isopods
Definition
mostly small aquatic crustaceans and terrestrial pill bugs
Term
decapods
Definition
lobsters, crayfish, crabs, shrimp. cuticle hardened by calcium carbonate
Term
copepods
Definition
plankton (barnacles?)
Term
echinoderms
Definition
sessile/slow-moving, water vascular system wiht network of hydraulic canals controls extension of tube feet - locomotion, feeding an dgas exchange. external fertilization. 
Term
sea stars (asteroidea)
Definition
arms radiating from central disk. evert stomach through mouth
Term
brittle stars (ophiuroidea)
Definition
distinct central disks: predators, scavengers, suspension feeders
Term
sea urchins and sand dollars (echinoidea
Definition
no arms but move slowly with rows of feet. complex jaw like structure
Term
sea lillies
Definition
live attached to the substrate by stalks. suspension feeding
Term
sea cucumbers (holothuroidea)
Definition
elongated animals - very different form all other echinoderms (only similarity is five rows of feet)
Term
protists
Definition
eukaryotic, primarily unicellular organisms. photo hetero or mixotrophs. 
Term
endosymbiosis
Definition
mitochondria evolved from endosymbiotic alpha proteobacteria within the earliest eukaryotes. all eukaryotes studied thus far have mitochondria or signs of having them in the past
Term
plastids
Definition
evolved from photosynthetic cyanoabacterium that became an endosymbiont of a heterotrophic eukaryote - led to red and green algae. 
Term
secondary endosymbiosis
Definition
red/green algae engulfed by heterotrophic eukaryote which led to new protist lineage
Term
6 supergroups of eukaryotes
Definition
excavates; chromalveolates; rhizaria; amoebozoans; opisthokonts; archaeplastida
Term
Excavata
Definition

protists with modified mitochondria and unique flagella.

include diplomonads, parabasalids, euglenozoans

Term
diplomonads
Definition
mitosomes lack functional ETC. ex: giardia intestinalis has two nuclei and multiple flagella
Term
parabasalids
Definition
reduced mitochondria = hydrogenosomes and generate energy anaerobically, releasing H2. Trichomonas vaginalis is a sexually transmitted parasite
Term
Euglenozoans
Definition

predatory hetero and autotrophs + pathogenic parasites (spiral/rod inside flagella).

large mitochondrion has mass of DNA = kinetoplast (chracteristics of kinetoplastids)

Term
euglenids
Definition
(euglenozoans) two flagella from anterior end. Switch to heterotrophy in the absence of sunlight
Term
chromalveolates
Definition

may have originated from secondary endosymbiosis (ancestor engulfed a red algae)

alveolates (dinaflgellates, apicomplexans, ciliates); stramenopiles (diatoms, golden and brown algae); oomycetes

Term
alveolates
Definition
membrane-bounded avleoli under the plasma membrane are characteristic of them - stabilize cell surface/osmoregulate. include: dinoflagellates, apicomplexans, ciliates
Term
dinoflagellates
Definition
unicellular. two flagella beat = spinning movement. largest proportion of marine and freshwater phytoplankton. *red tide. heterotrophic
Term
apicomplexans
Definition
animal parasites. complex life cycles that include both sex and asex, several host species. spread by tiny infectious sporozoites. apical complex of organelles specialized for invading host cells + apicoplast (nonphotosynthetic plastid)
Term
malaria
Definition
caused by plasmodium: insecticide resistance in anopheles mosquitos; drug resistant plasmodium; sequestering of parasite in human liver and blood cells; ability of parasite to change surface proteins
Term
ciliates
Definition
cilia used to move and feed. large macronuclei (metabolism and contains many genome copies) + small micronuclei (DNA). reproduce through binary fission - small nuclei are exchanged in conjugation which allows for genetic recombination
Term
Stramenopiles
Definition
several hetertrophs including algae. characterized by short smooth flagellum paired with longer hairy one
Term
diatoms
Definition
freshwater phytoplankton, with protective boxlike silica walls. unicellular - reproduce asexually. 
Term
golden and brown algae
Definition

golden: yellow and brown carotenoids, unicellular, biflagellated, marine and freshwater plankton

brown: largest and complex algae (seaweed - some have tissue and organs). seaweed have thallus (body) with rootlike holdfast and stemlike stripe that support leaflike blades

Term
alteration of generations
Definition
multicellular, haploid gametophyte produces gametes. after syngamy, diploid zygote grows into multicellular sporophyte, which produces spores by meiosis. gametophyte and sporophyte may appear similar (isomorphic) or different (heteromorphic)
Term
oomycetes
Definition

water olds, white rusts, downy mildews. no plastids. cell walls made of cellulose therefore not related to fungi. 

water mold eggs fertilized by a smaller sperm nucleus. zygotes germinate to form hyphae. important decomposers

rusts and mildews = destructive parasites of land parasites

Term
Rhizarians
Definition
chlorarachniophytes, forams, radiolarians. amoebas in rhizaria have threadlike pseudopodia
Term
forams
Definition
porous shells (tests), pseudopodia extend through pores for swimming. nourishment from symbiotic algae
Term
radiolarians
Definition
slender pseudopodia help organisms phagocytize microscopic food. primarily marine and have delicate silica shells
Term
archaeplastida
Definition
red, green algae, land plants
Term
red algae
Definition
marine, multicellular. alternation of generations, life cycles are diverse, no flagellated stages
Term
green algae
Definition
chloroplasts = those in green plants. chlorophytes (fresh water, unicell) and charophyceans (sex and asex, multicell= alt gen). size and complexity has increased: formation of colonies, repeated nuclear division to produce multinucleated filaments, cell division/differentiation to produce true multicellular forms
Term
unikonts
Definition
animals, fungi, protists - amoebozoans and opisthokonts
Term
amoebozoans
Definition
slime molds, gymnamoebas, entamoebas. resemblance of slime molds (mycetozoans) to fungi is a result of convergent evolution to similar lifestyles
Term
plasmodial slime molds
Definition
engulf food particles by phagocytosis. multinucleate mass = plasmodium is the feeding stage. harsh conditions: sporangia on erect stalks produce resistant spores by meiosis. spores germinate, amoeboid/flagellated haploid cells fuse, diploid nucleus divides to form new plasmodium
Term
cellular slime molds
Definition
haploid solitary amoeboid cells. as food is depleted, cells congregate into a mass. asexual fruiting bodies produce resistant spores. in sex, two amoebas fuse = zygote. after meiosis and mitosis, haploid amoebas are released. 
Term
opisthokonts
Definition
animals, fungi: nucleariids more closely related to fungi, choanoflagellates more close related to animals
Term
derived traits that distinguish terrestrial plants
Definition
apical meristems, alternation of generations (multicell, dependent embryo), walled spores in sporangia, multicellular gametangia
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