Kingdom Fungi:
-Mycology: study of fungi
1) One of Earth’s obscure lifeforms
- One spanning 86 acres, mostly underground, the Honey Mushroom (Armillaria ostoyae)
- One spanning 2000 acres in Oregon, another Honey Mushroom Honey Mushroom (Armillaria mellea)
-Resemble plants, but lack chloroplasts, so they don’t photosynthesize
-Are not animal, nor do they resemble bacteria or protozoa.
2) Microscopic in size to very large (mushrooms, mildew, molds and morels). Parasitic and saprophytic, major world decomposers.
Characteristics of Fungi:
A) General:
1) Major Decomposers along with bacteria
2) Can cause plant disease, accounting for millions of dollars in crop losses each year.
3) Can cause human diseases such as ringworm, athlete’s foot, and yeast infections (most yeasts filamentous)
B) Nutrition:
-Heterotrophic
-External Digestion: excrete enzymes which break down or “digest” food which is then absorbed by fungi.
1) Extensive network of hyphae provides an enormous surface area for absorption.
2) Animals are heterotrophic by digestion, fungi are heterotrophic by absorption.
-Most fungi are saprotrophic decomposers: break down waste products and dead remains of plants and animals.
-Some are parasitic: they live off the tissues of living plants and animals. (page 606, Figure 31.5)
C) Structure:
-Some are unicellular, such as yeast (not common).
-Most are multicellular eukaryotes.
1) Body (thallus) is a multicellular structure known as the mycelium.
2) A mycelium is a network of filaments called hyphae (page 605, Figure 31.3)
3) Hyphae (plural) Hypha (singular)- slender filaments
-Some have septa- crosswalls that divide the hyphae into cells.
-Septa only form a complete barrier when separating reproductive cells.
-Otherwise, the organism is multi-nucleated with cytoplasm flowing throughout the hyphae.
4) Types of hyphae:
-Heterokayotic: 2 genetically distinct nuclei in the same hyphae.
-Homokaryotic: hyphae with nuclei genetically the same
(Next two types used when discussing reproductive hyphae)
-Dikaryotic: 2 genetically distinct nuclei in the same cell
-Monokaryotic: one nucleus in each cell.
-Coenocytic: aseptate hyphae (no septa- no division between cells- like plasmodium, the "true" slime mold)
-Haustoria: specialized hyphae found in parasitic fungi that penetrates and absorbs nutrients directly from the cells of the host.
5) Cell walls consist of polysaccharides, including chitin, the same substance found in the outer structure of insects and crustaceans.
D) Reproduction:
-Asexual reproduction: involves spores or fragmentation of mycelium
-Sexual reproduction: can occur several ways:
1) Fusion of gametes released from gametangia (only in Ascomycota)
2) Penetration of gametes (or gamete) into the gametangium (only in Basidiomycota).
3) Fusion of gametangia (Zygomycota).
-Both sexual and asexual reproduction produce spores, ensuring dispersal of the species. All spores nonmotile.
E) Four Phyla of Fungi: Classification based on the features related to sexual reproduction.
1) Phylum Chytridiomycota:
-Chytrids (common name)
-Oldest fossil fungi, are the sister phylum to the remaining fungal phyla, found in northern Russia
-Predominantly aquatic
-Only fungus that has flagellated gametes
-The closest relative to fungi in the Kingdom Protista also have flagella.
-One species has been tied to the decline in frog populations worldwide (once classifies as a protist), parasitic.
Lab Example: Allomyces.
2) Phylum Zygomycota:
-Commonly known as zygomycetes
-Approximately 1050 species (small phylum).
-Saprotrophs, living off plant and animal remains in the soil or bakery goods.
-Hyphae are multinucleate, lack septa (except where involved with reproduction).
Lab Example: Rhizopus stolonifer- black bread mold. Distinct characteristics: zygosporangium- results from fusion of gametangia. (page 608, Figure 31.7)
3) Phylum Ascomycota:
-Commonly known as ascomycetes, sac fungi.
-Examples:
a) yeast- unicellular oddity
b) morels- are not mushrooms
c) truffles
d) powdery mildews
-Plant pathogens: Ophiostoma ulmi is the organism that causes Dutch Elm Disease (The organism that causes Chestnut Blight is in this phylum also).
-Distinct characteristics:
a) Formation of conidia- structure (spores) formed during asexual reproduction
b) Formation of ascus- sac-like structure where the zygote is formed, sexual reproduction (pages 610-611, Figure 31.9)
-Yeast: most reproduce asexually via cell fission or budding
a) Most economically useful fungus
b) Used for baking/beer (Saccharomyces cerevisiae)/ wine
c) Are eukaryotic cell of choice for genetic and biomedical research (rapid generation time).
d) Yeast infections: candida, thrush
4) Phylum Basidiomycota
-Known as basidiomycetes, club fungi
-Examples: mushrooms, toadstools, puffballs, jelly fungi, and shelf fungi.
-Plant pathogens: rusts and smuts (rusts are brightly colored and smuts look like a black smudge)
-Distinct characteristics:
a) Sexual reproductive structure: basidium, which is a club-shaped spore and is located under the cap of the mushroom or in the tubes at the base of pores in shelf fungi.
-Examples:
a) Birds nest fungi's basidiospore is dispersed by raindrops
b) Stinkhorn- Phallus impudicus, emits a disagreeable odor which attracts files who unintentionally pick up spores and distribute them.
c) Smuts and rusts are club fungi that parasitize cereal crops.
-Rusts often require two different host plants to complete their life cycle; such as apple and juniper.
-Example: Black stem rust of wheat, requires barberry bushes. Blister rust of white pine and black currant.
-Other interesting mushrooms:
a) Agaricus capestris: field mushroom; commercially grown species.
b) Amanita phalloides: destroying, death angel (10-12 hours after consumption = death)
c) Psilocybe mexicanna: used by Mexican Indians for religious ceremonies (contains psilocybin, which is structurally like LSD or mescaline)
d) Claviceps purpurea: ergot fungus, infects rye. Alkaloids from this fungus are used in medicine to cause uterine contraction and to treat circulatory disorders such as migraine headaches. Causes ergotism which is thought to be the cause of the frenzy surrounding the Salem witch trials (lysergic acid)
E) Fungal Associations:
1) Lichens:
-A symbiotic association between fungus (mostly ascomycetes) and a photosynthetic partner (cyanobacteria, green algae, or both).
3 Types:
a) Crustose: compact, found on bare rocks or tree bark
b) Foliose: leaf-like
c) Fruticose: shrub-like (stalked)
-Lichen are indicators of air pollution
Lab Examples: Assorted specimens, slides of Physcis
2) Mycorrhizae
-Greek: Mykes = fungus, Rhizion = root
-Symbiotic association between fungi and plant roots, in about 90% of plants.
-Gives greater absorptive surface for intake of minerals and water
a) replace and perform the same function as root hairs.
b) Important because it helps create larger crops
-2 Types:
a) Endomycorrhizae: (arbuscular mycorrhizae) The fungus is usually a zygomycete. Hyphae penetrate the plant's roots (roughly 200,000 associations of this kind)
b) Ectomycorrhizae: Do not penetrate plant root cells, usually a basidiomycetes.
Example: Truffle- mycorrhizal fungus living in association with oak and beech tree roots. (ascomycete)
(page 616, Figure 31.16)
Sunday, September 26, 2010
End of Protista:
Phylum Apicomplexa:
1) Sporozoans
2) Nonmotile
3) Form spores (parasites)
4) Organelles, nucleus, etc. located at anterior of cell (apical complex)
5) Reproduction: sexual, asexual and alternation of generations
Lab Example: Plasmodium (4 species of this organism cause malaria) Vector: mosquito. 40% of the world’s population live where malaria is endemic. (pg. 570, Figure 29.13)
Molds:
Phylum Acrasiomycota:
1) Cellular slime molds
2) Fresh water, damp soil, rotting vegetation
3) Related to amoebas
4) Individual organisms initially, later in life cycle individuals aggregate and form a slug (pg. 577-578, Figure 29.31)
Phylum Myxomycota:
1) Plasmodial slime- known as “true” slime molds
2) Found on forest floor (they like shade)
3) Plasmodium (a structure): a brightly colored, nonwalled, multinucleated mass of cytoplasm.
-Engulfs and digests bacteria and yeast and other small, organic matter as they move along the forest floor.
-Members form a coenocytic (multinucleated) structure known as a plasmodium.
Lab Example: Physarum (cause mustard plant disease) commonly known as devil droppings and clubroot. Have asexual spores called swarm cells, plasmogomy.
Phylum Oomycota:
1) Oomycetes
2) Fresh or saltwater, soil.
3) Water molds, white rusts, downy mildews (on grapes, lettuce, corn, cabbage)
4) Parasites and saprophytic on fish, plants, and insects.
5) 2 unequal flagella
6) Motile spores- zoospore
7) Asexual and sexual reproduction, not alternation of generations (pg 578, Figure 29.30)
1) Sporozoans
2) Nonmotile
3) Form spores (parasites)
4) Organelles, nucleus, etc. located at anterior of cell (apical complex)
5) Reproduction: sexual, asexual and alternation of generations
Lab Example: Plasmodium (4 species of this organism cause malaria) Vector: mosquito. 40% of the world’s population live where malaria is endemic. (pg. 570, Figure 29.13)
Molds:
Phylum Acrasiomycota:
1) Cellular slime molds
2) Fresh water, damp soil, rotting vegetation
3) Related to amoebas
4) Individual organisms initially, later in life cycle individuals aggregate and form a slug (pg. 577-578, Figure 29.31)
Phylum Myxomycota:
1) Plasmodial slime- known as “true” slime molds
2) Found on forest floor (they like shade)
3) Plasmodium (a structure): a brightly colored, nonwalled, multinucleated mass of cytoplasm.
-Engulfs and digests bacteria and yeast and other small, organic matter as they move along the forest floor.
-Members form a coenocytic (multinucleated) structure known as a plasmodium.
Lab Example: Physarum (cause mustard plant disease) commonly known as devil droppings and clubroot. Have asexual spores called swarm cells, plasmogomy.
Phylum Oomycota:
1) Oomycetes
2) Fresh or saltwater, soil.
3) Water molds, white rusts, downy mildews (on grapes, lettuce, corn, cabbage)
4) Parasites and saprophytic on fish, plants, and insects.
5) 2 unequal flagella
6) Motile spores- zoospore
7) Asexual and sexual reproduction, not alternation of generations (pg 578, Figure 29.30)
Wednesday, September 8, 2010
Lab 25, part 4
Phylum Chrysophyta (Golden-Brown Algae):
-Diatoms: unicellular algae with chlorophyll a and chlorophyll c; pigment: xanthophyll
-Photosynthetic
-Have a hard cell wall made of silicon-dioxide
-Pillbox and radial shapes
-Cell wall persists long after the organism dies, accumulate in layers of diatomaceous earth.
Lab Examples:
-Cyclotella:
Phylum Pyrrhophyta (Dinoflagellates):
-Unicellular
-Cellulose plates give them strange shapes, like armor
-Two flagella located in perpendicular grooves
-Cause red tide: Ptychodiscus bruvis. Blooms of algae that deplete oxygen and produce toxins that kill massive numbers of fish.
-Primary producers in oceans, second only to diatoms
-Heterotrophic or autotrophic, some are bioluminescent.
Lab Examples:
-Peridinium:
-Ceratium:
Phylum Euglenophyta (Euglenoids):
-Unicellular, motile, have two flagella
-Unique in that some are autotrophic, some are heterotrophic, some saprophytic, depending on environmental conditions.
-Chlorophylls a and b
-Distinctive because cell walls are made mostly of protein, which allows for flexibility
-Colored eyespot, for detection of light, near the base of the flagella
Lab Example:
-Euglena:
-Diatoms: unicellular algae with chlorophyll a and chlorophyll c; pigment: xanthophyll
-Photosynthetic
-Have a hard cell wall made of silicon-dioxide
-Pillbox and radial shapes
-Cell wall persists long after the organism dies, accumulate in layers of diatomaceous earth.
Lab Examples:
-Cyclotella:
Phylum Pyrrhophyta (Dinoflagellates):
-Unicellular
-Cellulose plates give them strange shapes, like armor
-Two flagella located in perpendicular grooves
-Cause red tide: Ptychodiscus bruvis. Blooms of algae that deplete oxygen and produce toxins that kill massive numbers of fish.
-Primary producers in oceans, second only to diatoms
-Heterotrophic or autotrophic, some are bioluminescent.
Lab Examples:
-Peridinium:
-Ceratium:
Phylum Euglenophyta (Euglenoids):
-Unicellular, motile, have two flagella
-Unique in that some are autotrophic, some are heterotrophic, some saprophytic, depending on environmental conditions.
-Chlorophylls a and b
-Distinctive because cell walls are made mostly of protein, which allows for flexibility
-Colored eyespot, for detection of light, near the base of the flagella
Lab Example:
-Euglena:
Lab 25, part 3
Phylum Streptophyta (Chara)
(Not in Lab Manual)
-Chara: Also known as stonewort, or brittlewort.
-They are the precursors to land plants, where land plants came from
-Secrete a calcium carbonate, white lime coating.
-Reproduces with oogonia and antheridia.
Lab Examples:
-Chara:
-Reproductive structures: Larger structure is oogonium and smaller is antheridium
(Not in Lab Manual)
-Chara: Also known as stonewort, or brittlewort.
-They are the precursors to land plants, where land plants came from
-Secrete a calcium carbonate, white lime coating.
-Reproduces with oogonia and antheridia.
Lab Examples:
-Chara:
-Reproductive structures: Larger structure is oogonium and smaller is antheridium
Lab 25, part 2
Phylum Phaeophyta (Brown Algae):
-Largest of the algae, usually more complex (no unicellular or colonial types).
-Brown pigment: fucoxanthin
-Important food crop, especially Laminaria, kelp sold as "kombu"
-Brown algae produce alginic acid (hydrophilic; absorbs lots of water), commercially used as an emulsifier
Lab Examples:
-Chondrus crispus
-Corraline:
-Fucus: commonly known as rockweed, outer surface covered in a gelatinous sheath to suit to its environment of pounding ocean waves. Has a blade that resembles a plant leaf, a stipe that resembles a stem, and a holdfast that resembles a root. Has reproductive structures called conceptacles that contain oogonia (female) and antheridia (male) reproductive cells.
-Laminaria (kelp):
Macrocystis:
Nereocystis:
Sargassum:
Phylum Rhodophyta (Red Algae):
-Red pigment from phycobilins in their plastids
-Thallus of a red alga can be attached, free floating, filamentous, or parenchymatous (fleshy)
-Common red alga extract: agar, extracted from seaweeds such as Gracilaria.
Lab Examples:
-Agardhiella:
-Gracilaria:
-Polysiphonia:
Porphyra:
-Largest of the algae, usually more complex (no unicellular or colonial types).
-Brown pigment: fucoxanthin
-Important food crop, especially Laminaria, kelp sold as "kombu"
-Brown algae produce alginic acid (hydrophilic; absorbs lots of water), commercially used as an emulsifier
Lab Examples:
-Chondrus crispus
-Corraline:
-Fucus: commonly known as rockweed, outer surface covered in a gelatinous sheath to suit to its environment of pounding ocean waves. Has a blade that resembles a plant leaf, a stipe that resembles a stem, and a holdfast that resembles a root. Has reproductive structures called conceptacles that contain oogonia (female) and antheridia (male) reproductive cells.
-Laminaria (kelp):
Macrocystis:
Nereocystis:
Sargassum:
Phylum Rhodophyta (Red Algae):
-Red pigment from phycobilins in their plastids
-Thallus of a red alga can be attached, free floating, filamentous, or parenchymatous (fleshy)
-Common red alga extract: agar, extracted from seaweeds such as Gracilaria.
Lab Examples:
-Agardhiella:
-Gracilaria:
-Polysiphonia:
Porphyra:
Lab 25, part 1
Protista (The Algae)
-First of the four kingdoms of domain Eukarya, the oldest and most diverse kingdom in this domain. Usually divided into three general groups: algae, protozoans, and slime molds.
-Algae is a main oxygen producer and food source.
-Photosynthetic.
-Major groups of algae distinguished by their pigments: substances that absorb light. 4 types:
-Red algae
-Green algae
-Brown algae
-Golden-brown algae.
Cellular Organization, 3 types:
-Unicellular: single cells
-Filamentous: chains of cells
-Colonial: groups of cells attached in a non-chain like way
-A few are multicellular
Phylum Chlorophyta (Green Algae):
-contain chlorophyll a, and chlorophyll b
Lab Examples:
-Chlamydomonas: motile, unicellular, found in soil, lakes and ditches. Has a stigma, which is a reddish colored spot, that absorbs light. Its movement is jerky due to the flagella.
-Chlamydomonas reproduces via alternation of generations. More on this later.
-Spirogyra: filamentous, found in fresh water, has a slippery texture. Reproduces via conjugation. More on this later.
-Cladophora: branched, filamentous, also found in fresh water. Has a coarser texture than Spirogyra. Reproduces via alternation of generations.
-Volvox: colonial, many small, round cells bound in a spherical matrix. Some cells specialize and can make sperm and eggs. Reproduces via oogamy. Motile sperm swim to and merge with the large, non-motile eggs to form a diploid zygote. During asexual reproduction, some cells of Volvox bulge inward and produce colonies called daughter colonies that are contained within the parent colony.
-First of the four kingdoms of domain Eukarya, the oldest and most diverse kingdom in this domain. Usually divided into three general groups: algae, protozoans, and slime molds.
-Algae is a main oxygen producer and food source.
-Photosynthetic.
-Major groups of algae distinguished by their pigments: substances that absorb light. 4 types:
-Red algae
-Green algae
-Brown algae
-Golden-brown algae.
Cellular Organization, 3 types:
-Unicellular: single cells
-Filamentous: chains of cells
-Colonial: groups of cells attached in a non-chain like way
-A few are multicellular
Phylum Chlorophyta (Green Algae):
-contain chlorophyll a, and chlorophyll b
Lab Examples:
-Chlamydomonas: motile, unicellular, found in soil, lakes and ditches. Has a stigma, which is a reddish colored spot, that absorbs light. Its movement is jerky due to the flagella.
-Chlamydomonas reproduces via alternation of generations. More on this later.
-Spirogyra: filamentous, found in fresh water, has a slippery texture. Reproduces via conjugation. More on this later.
-Cladophora: branched, filamentous, also found in fresh water. Has a coarser texture than Spirogyra. Reproduces via alternation of generations.
-Volvox: colonial, many small, round cells bound in a spherical matrix. Some cells specialize and can make sperm and eggs. Reproduces via oogamy. Motile sperm swim to and merge with the large, non-motile eggs to form a diploid zygote. During asexual reproduction, some cells of Volvox bulge inward and produce colonies called daughter colonies that are contained within the parent colony.
Lab 24, part 2
Cyanobacteria
-Prokaryotic.
-Formerly known as Blue-Green Algae, but this is a misnomer, they are not algae, but are bacteria.
-Photosynthetic, with pigments chlorophyll a and the accessory pigments phycocyanin (blue) and phycoerythrin (red).
-Reproduce by fission.
-Surrounded by a jellylike sheath.
Lab Examples:
1) Oscillatoria, looks like green spaghetti under the microscope. Grows in long chains called trichomes.
2) Nostoc, commonly called witch's butter or starjelly. Forms large, grape-like colonies. Trichomes consist of small vegetative cells and larger, thick-walled heterocysts in which nitrogen fixation occurs. Looks like a green, beaded necklace.
3) Gloeocapsa, characterized by a thick, gelatinous sheath enclosing vegetative cells. Form clusters of cells and therefore has a colonial body form.
4) Merismopedia, also forms colonies of tiny, green, spherical clusters in rectangular shapes.
-Prokaryotic.
-Formerly known as Blue-Green Algae, but this is a misnomer, they are not algae, but are bacteria.
-Photosynthetic, with pigments chlorophyll a and the accessory pigments phycocyanin (blue) and phycoerythrin (red).
-Reproduce by fission.
-Surrounded by a jellylike sheath.
Lab Examples:
1) Oscillatoria, looks like green spaghetti under the microscope. Grows in long chains called trichomes.
2) Nostoc, commonly called witch's butter or starjelly. Forms large, grape-like colonies. Trichomes consist of small vegetative cells and larger, thick-walled heterocysts in which nitrogen fixation occurs. Looks like a green, beaded necklace.
3) Gloeocapsa, characterized by a thick, gelatinous sheath enclosing vegetative cells. Form clusters of cells and therefore has a colonial body form.
4) Merismopedia, also forms colonies of tiny, green, spherical clusters in rectangular shapes.
Lab 24, part 1
Bacteria
-Bacteria are prokaryotes.
prokaryotes: species with cells lacking membrane-enclosed organelles. Unicellular; cell size of about 1 micrometer in diameter; DNA molecule in nucleoid region, not nucleus; reproduce by binary fission; simpler flagella; wide metabolic diversity.
eukaryotes: species with cells that have membrane-enclosed organelles. Multicellular; cell size of about 10 micrometers; DNA in chromosomes in nucleus; cell division via mitosis and meiosis; more complex flagella; less metabolic diversity.
Domain Archaea (with Kingdom Archaebacteria)
-extremophiles
Domain Bacteria (with Kingdom Bacteria)
-Distributed more widely than any other group of organisms.
-Have cell walls which give them three distinct shapes:
1) Bacillus (rod-shaped)
2) Coccus (spherical)
3) Spirillum (spiral)
-Mostly Heterotrophic, decomposers that feed on dead organic matte and release nutrients locked in dead tissue.
-Some Autotrophic, via photosynthesis.
-Fission: asexual reproduction in which a cell's DNA replicates and the cell pinches in half without the nuclear and chromosomal events associated with mitosis.
-Conjugation: genetic recombination in which all or part of the genetic material of one bacterium is transferred to another bacterium and a new set of genes is assembled.
-Some bacteria are pathogenic and cause diseases: pneumonia, tuberculosis.
-Gram Stain: a helpful process that correlates with the sensitivity of a bacterium to antibiotics.
1) Gram-negative: bacteria that have a thinner cell wall that does not retain the crystal violet dye applied in the process of staining. After the process, they will be red from safranin. (Have a lipopolysaccharide coating).
2) Gram-positive: bacteria that have a thicker cell wall that does retain the crystal violet dye. (Have not lipopolysaccharide coating, just peptidoglycan).
-Bacterial Colony Morphology: Can help identify bacteria by looking at shape, color, size, texture and margins of a colony
1) Form:
a) Circular
b) Pinpoint
c) Irregular and spreading
d) Filamentous
e) Wrinkled
2) Margins:
a) Smooth (entire)
b) Wavy (undulate)
c) Lobate
d) Irregular (erose)
e) Filamentous
3) Elevations:
a) Flat
b) Raised
c) Convex
d) Umbonate
-Nitrogen Fixation By Bacteria: the process by which atmospheric nitrogen (N2) is transformed into other nitrogenous compounds that can be used as nutrients by plants. Because the triple bond in the nitrogen molecule is hard to break, plants depend on bacteria to do this.
-Use an enzyme called nitrogenase along with ATP, energized electrons, and water to convert N2 to ammonia (NH3). Ammonia can be absorbed by plants and used to make proteins and other macromolecules.
Lab Example: Rhizobium, grows on the roots of legumes. Form nodules that transfer ammonia to the host plant while the host plants supplies the bacteria with sugars and other nutrients.
Bacterial Sensitivity to Inhibitors:
-Determined by Sensitivity Plates: a petri dish of solid medium uniformly inoculated with a bacterium.
After inoculation, four to eight small paper disks that have each been soaked in a different antibiotic are placed equidistant on the inoculated surface. After 24 hours, an effective antibiotic will produce a visible halo of clear surface around the disks where it inhibited growth of bacteria. If the antibiotic was ineffective, the bacteria will grow to the edge of the paper disk.
-Bacteria are prokaryotes.
prokaryotes: species with cells lacking membrane-enclosed organelles. Unicellular; cell size of about 1 micrometer in diameter; DNA molecule in nucleoid region, not nucleus; reproduce by binary fission; simpler flagella; wide metabolic diversity.
eukaryotes: species with cells that have membrane-enclosed organelles. Multicellular; cell size of about 10 micrometers; DNA in chromosomes in nucleus; cell division via mitosis and meiosis; more complex flagella; less metabolic diversity.
Domain Archaea (with Kingdom Archaebacteria)
-extremophiles
Domain Bacteria (with Kingdom Bacteria)
-Distributed more widely than any other group of organisms.
-Have cell walls which give them three distinct shapes:
1) Bacillus (rod-shaped)
2) Coccus (spherical)
3) Spirillum (spiral)
-Mostly Heterotrophic, decomposers that feed on dead organic matte and release nutrients locked in dead tissue.
-Some Autotrophic, via photosynthesis.
-Fission: asexual reproduction in which a cell's DNA replicates and the cell pinches in half without the nuclear and chromosomal events associated with mitosis.
-Conjugation: genetic recombination in which all or part of the genetic material of one bacterium is transferred to another bacterium and a new set of genes is assembled.
-Some bacteria are pathogenic and cause diseases: pneumonia, tuberculosis.
-Gram Stain: a helpful process that correlates with the sensitivity of a bacterium to antibiotics.
1) Gram-negative: bacteria that have a thinner cell wall that does not retain the crystal violet dye applied in the process of staining. After the process, they will be red from safranin. (Have a lipopolysaccharide coating).
2) Gram-positive: bacteria that have a thicker cell wall that does retain the crystal violet dye. (Have not lipopolysaccharide coating, just peptidoglycan).
-Bacterial Colony Morphology: Can help identify bacteria by looking at shape, color, size, texture and margins of a colony
1) Form:
a) Circular
b) Pinpoint
c) Irregular and spreading
d) Filamentous
e) Wrinkled
2) Margins:
a) Smooth (entire)
b) Wavy (undulate)
c) Lobate
d) Irregular (erose)
e) Filamentous
3) Elevations:
a) Flat
b) Raised
c) Convex
d) Umbonate
-Nitrogen Fixation By Bacteria: the process by which atmospheric nitrogen (N2) is transformed into other nitrogenous compounds that can be used as nutrients by plants. Because the triple bond in the nitrogen molecule is hard to break, plants depend on bacteria to do this.
-Use an enzyme called nitrogenase along with ATP, energized electrons, and water to convert N2 to ammonia (NH3). Ammonia can be absorbed by plants and used to make proteins and other macromolecules.
Lab Example: Rhizobium, grows on the roots of legumes. Form nodules that transfer ammonia to the host plant while the host plants supplies the bacteria with sugars and other nutrients.
Bacterial Sensitivity to Inhibitors:
-Determined by Sensitivity Plates: a petri dish of solid medium uniformly inoculated with a bacterium.
After inoculation, four to eight small paper disks that have each been soaked in a different antibiotic are placed equidistant on the inoculated surface. After 24 hours, an effective antibiotic will produce a visible halo of clear surface around the disks where it inhibited growth of bacteria. If the antibiotic was ineffective, the bacteria will grow to the edge of the paper disk.
Chapters 29, 30 cont. Phylum Chrysophyta-Ciliophora
E) Phylum Chrysophyta:
1) Diatoms and Golden Algae- both have chloroplasts
2) Both diatoms and golden algae have chrysolaminarin- a carbohydrate that yields glucose that other organisms use for food
3) Fresh and marine water
4) Unicellular
5) Golden algae: yellow/brown carotenoid, xanthophyll pigment- fights oxidative DNA damage.
6) Diatoms: double shelled, remember the pillbox shape, made out of silica; chlorophylls a and c, and carotenoids
7) Reproduction: asexually and under extreme conditions, sexually.
Lab Examples: Diatom: bilateral (pinnate, 2 sided) and radial (centric, like a wheel).
(See page 574-575 in book)
Remember: “Chrysophyta” looks like the word “Crystals” = Diatoms made of glass, or Diatoms sounds like diamonds
F) Phylum Pyrrhophyta:
(formerly dinoflegellata, still commonly known as dinoflagellates)
1) Fresh and marine water (some phosphorescent)
2) Unicellular
3) Two flagella perpendicular to each other
–Looks like they’re armor-plated, see page 569, Figure 29.11
4) Most have chlorophylls a and c
5) Primary food source in warmer oceans
6) Red tides- produces toxin
7) Reproduction: Longitudinal cell division and some sexual reproduction under extreme conditions.
-Remember longitudinal means long ways up and down, and transverse means short ways across.
Lab Examples: Peridinium and Ceratium
Remember: “Pyrrhophyta” looks like the word “Pyro” = Red tides of fiery poison
G) Phylum Euglenophyta:
1) Euglenoids
2) Fresh water only
3) 1/3 have chloroplasts and are autotrophic (these are the individuals we saw in lab)
4) 2/3 have no chloroplasts and are heterotrophic (includes saprophytic)
5) All are unicellular
6) No cell wall, has a pellicle, crosshatches of protein, flexible for movement (just like the Paramecium)
7) Eyespot/Stigma: detects light, which the organism needs to find to undergo photosynthesis
Lab Example: Euglena
(See page 567, Figure 29.8)
*Protozoan and Molds
A) Phylum Rhizopoda:
1) Amoebas
2) Found in fresh and salt water, and in soil
3) Reproduction by fission (no sexuality)
4) Unicellular
5) No cell wall, no flagella
6) Movement by extension of cytoplasm
-Pseudopod (plural pseudopodia) “fake foot”
(See page 576, Figure 29.25)
7) Heterotrophic (eats by phagocytosis, whereby it engulfs its meal, and drinks by pinocytosis where it engulfs fluids)
Lab Examples: Entamoeba histolytica (causes amoebic dysentery); Difflugia and Arcello.
Remember: “Rhizopoda” has “podia” = feet = strange movement via pseudopodia
B) Phylum Foraminifera:
1) Commonly known as Forams
2) Marine only, found on ocean floors (look like seashells)
-incredible numbers
-Egyptian pyramids and white cliffs of Dover are built of foraminiferan limestone.
3) Reproduction: alternation of generations
4) Unicellular
5) No cell wall or flagella
6) Pore-studded shells called tests
-Projection called podia (or poda) “feet”, thin streams of cytoplasm
-Podia extends out of pores
-Used for swimming, grabbing particles for eating or attachment
Remember: “Foraminifera” contains the word “Mini” = Mini seashells
C) Phylum Sarcomastigophora:
1) Commonly known as zoomastigotes (animal-like)
2) Unicellular
3) Heterotrophic
4) Have at least 1 flagellum
5) Free living and parasitic forms
6) Reproduction: Majority reproduce asexually
Lab Example: Trypanosoma- responsible for African Sleeping Sickness, the vector for this illness is the tsetse fly.
Remember: “Sarcomastigophora” contains the word “Sarcoma” = malignant = parasitic disease African Sleeping Sickness
D) Phylum Ciliophora:
1) Ciliates
2) Unicellular, have pellicle (just like Euglena)
3) Heterotrophic
4) Have a large number of cilia
-Cilium (singular)- a short, cellular projection, much like a shorter, thicker flagellum)
5) Reproduction: Paramecium Example:
-Asexual: By transverse fission, for 500-600 generations until the genetic material is worn out. Then it reverts to:
-Sexual: By conjugation. They are easy prey when conjugating, which can take up to several hours.
-All ciliates have a macronucleus for physiological functions and a micronucleus for sexual reproduction. It is important to know the difference for the test (page 572, Figures 29.16 and 29.17. Fully understand conjugation).
Lab Example: Paramecium, Vorticella (flower-like bell on a retractable stalk, a filter feeder); Stentor.
Remember: “Ciliophora” organisms have lots of “Cilia”
1) Diatoms and Golden Algae- both have chloroplasts
2) Both diatoms and golden algae have chrysolaminarin- a carbohydrate that yields glucose that other organisms use for food
3) Fresh and marine water
4) Unicellular
5) Golden algae: yellow/brown carotenoid, xanthophyll pigment- fights oxidative DNA damage.
6) Diatoms: double shelled, remember the pillbox shape, made out of silica; chlorophylls a and c, and carotenoids
7) Reproduction: asexually and under extreme conditions, sexually.
Lab Examples: Diatom: bilateral (pinnate, 2 sided) and radial (centric, like a wheel).
(See page 574-575 in book)
Remember: “Chrysophyta” looks like the word “Crystals” = Diatoms made of glass, or Diatoms sounds like diamonds
F) Phylum Pyrrhophyta:
(formerly dinoflegellata, still commonly known as dinoflagellates)
1) Fresh and marine water (some phosphorescent)
2) Unicellular
3) Two flagella perpendicular to each other
–Looks like they’re armor-plated, see page 569, Figure 29.11
4) Most have chlorophylls a and c
5) Primary food source in warmer oceans
6) Red tides- produces toxin
7) Reproduction: Longitudinal cell division and some sexual reproduction under extreme conditions.
-Remember longitudinal means long ways up and down, and transverse means short ways across.
Lab Examples: Peridinium and Ceratium
Remember: “Pyrrhophyta” looks like the word “Pyro” = Red tides of fiery poison
G) Phylum Euglenophyta:
1) Euglenoids
2) Fresh water only
3) 1/3 have chloroplasts and are autotrophic (these are the individuals we saw in lab)
4) 2/3 have no chloroplasts and are heterotrophic (includes saprophytic)
5) All are unicellular
6) No cell wall, has a pellicle, crosshatches of protein, flexible for movement (just like the Paramecium)
7) Eyespot/Stigma: detects light, which the organism needs to find to undergo photosynthesis
Lab Example: Euglena
(See page 567, Figure 29.8)
*Protozoan and Molds
A) Phylum Rhizopoda:
1) Amoebas
2) Found in fresh and salt water, and in soil
3) Reproduction by fission (no sexuality)
4) Unicellular
5) No cell wall, no flagella
6) Movement by extension of cytoplasm
-Pseudopod (plural pseudopodia) “fake foot”
(See page 576, Figure 29.25)
7) Heterotrophic (eats by phagocytosis, whereby it engulfs its meal, and drinks by pinocytosis where it engulfs fluids)
Lab Examples: Entamoeba histolytica (causes amoebic dysentery); Difflugia and Arcello.
Remember: “Rhizopoda” has “podia” = feet = strange movement via pseudopodia
B) Phylum Foraminifera:
1) Commonly known as Forams
2) Marine only, found on ocean floors (look like seashells)
-incredible numbers
-Egyptian pyramids and white cliffs of Dover are built of foraminiferan limestone.
3) Reproduction: alternation of generations
4) Unicellular
5) No cell wall or flagella
6) Pore-studded shells called tests
-Projection called podia (or poda) “feet”, thin streams of cytoplasm
-Podia extends out of pores
-Used for swimming, grabbing particles for eating or attachment
Remember: “Foraminifera” contains the word “Mini” = Mini seashells
C) Phylum Sarcomastigophora:
1) Commonly known as zoomastigotes (animal-like)
2) Unicellular
3) Heterotrophic
4) Have at least 1 flagellum
5) Free living and parasitic forms
6) Reproduction: Majority reproduce asexually
Lab Example: Trypanosoma- responsible for African Sleeping Sickness, the vector for this illness is the tsetse fly.
Remember: “Sarcomastigophora” contains the word “Sarcoma” = malignant = parasitic disease African Sleeping Sickness
D) Phylum Ciliophora:
1) Ciliates
2) Unicellular, have pellicle (just like Euglena)
3) Heterotrophic
4) Have a large number of cilia
-Cilium (singular)- a short, cellular projection, much like a shorter, thicker flagellum)
5) Reproduction: Paramecium Example:
-Asexual: By transverse fission, for 500-600 generations until the genetic material is worn out. Then it reverts to:
-Sexual: By conjugation. They are easy prey when conjugating, which can take up to several hours.
-All ciliates have a macronucleus for physiological functions and a micronucleus for sexual reproduction. It is important to know the difference for the test (page 572, Figures 29.16 and 29.17. Fully understand conjugation).
Lab Example: Paramecium, Vorticella (flower-like bell on a retractable stalk, a filter feeder); Stentor.
Remember: “Ciliophora” organisms have lots of “Cilia”
Monday, September 6, 2010
Chapters 29-30: Protista
Protista
1) Eukaryotic
a) Greek for "true nucleus"(good kernel).
b) More than 10 micrometers in diameter
c) Elaborate shapes (branch, filamentous, tetrahedral, etc.)
2) Unicellular, multicellular, and colonial.
3) Sexuality evolved with this Kingdom.
4) Ancestors of plants, fungus, and animals.
Transition Between Prokaryotes and Eukaryotes:
Pelomyxa palustris: the only member of Phylum Caryoblastea
1) Single-celled ameboid protist, lives at the bottom of ponds.
2) Nucleus divides more like a prokaryote than a eukaryote.
3) No mitochondria; has bacteria living in it that serve a similar purpose.
Endosymbiotic Bacteria:
1) Live within other cells, perform specific functions for thir host.
2) Endosymbiotic Theory by Lynn Margulis of University of Mass. in the 1960's.
a) Theory states that a critical stage in evolution of the eukaryote cells involved endosymbiotic relationships with prokaryotic organisms (bacteria).
b)Energy-producing bacteria may have come to reside within larger bacteria, eventually evolving into mitochondria (powerhouse).
c) Photosynthetic bacteria may have come to live in association with other larger bacteria, leading to the evolution of chloroplasts- the photosynthetic organelles of plants and algae.
d) Bacteria with flagella may have become symbiotically involved with non-flagellated bacteria, producing larger, motile cells.
Photosynthetic Protists (Algae):
A) Phylum Chlorophyta:
1)Green Algae
-Once incorrectly believed to have given rise to land plants
-Cells of Chlorophyta contain organelles called chloroplasts in which photosynthesis occurs.
-Photosynthetic pigments are chlorophyll a and chlorophyll b and various carotenoids.
-They are the same as those found in plants and are found in similar proportions.
2) Most aquatic- found in fresh and salt water (but not all)
3) Unicellular, filamentous and colonial
-Those that are motile have two apical (tip) or sub-apical flagella.
-Terrestrial algae occurs on moist trunks of trees, moist soil, moist rocks (even on snow).
-Various species are highly specialized, some living exclusively on turtles, green sloths of Costa Rica, or within the gill mantles of marine mollusks.
4) Reproduction in green algae is asexual and sexual: Alternation of Generations
(How things reproduce is a big part of evolution)
a) First phase produces spores - sporophyte (2n, diploid)
b) Second phase produces gametes - gametophyte (1n, haploid)
Lab Examples: Chlamydomonas- has a red eye-spot; Volvox, forms colonies 500-60,000 organisms that act as one unit; Spirogyra and Cladophora- filamentous
B) Phylum Streptophyta (Chara)
Stoneworts (Brittleworts) with calcium carbonate/limestone secretions
(See Figure 30.1, page 582)
1) Precursor to land plants
2) 450 million years old
3) Ancient fossils same as today
4) They are encrusted with white lime
5) Grow several feet tall, slender, threadlike, with whorls of branches a few inches in length
6) Found in fresh water or mildly brackish water (in estuaries)
7) 3 things that make them unique:
a) Unlike most algae which consist of single cells, simple colonies, or chains, stoneworts grow upwards; branches come off of giant central cells.
- giant cells contain many nuclei, are several times the width of a human hair, and an inch or more in length.
b) They have a relatively advanced feature of sexual reproduction which uses eggs and sperm.
c) Their biochemical processes are more similar to land plants than other green algae.
C) Phylum Phaeophyta
1) Brown algae
2) Marine, largest of the algae; kelp. Found worldwide.
-Unique ability to withstand pounding tides due to holdfasts and mucilaginous cell walls.
3) Multicellular
4) Blade: (not a leaf) but leaf like; stipe: resembles a stem; holfasts: resemble roots.
5) Chlorophyll a and c; pigment fucoxanthin (may slow prostate cancer).
6) Reproduction by alternation of generations
7) Economically important: food, fertilizer, iodine, salts, alginic acids (used as an emulsifier in dripless paint, ice cream, pudding mixes, etc.). An emulsifier allows water and oil to mix.
Lab Examples: Fucus and Laminaria
D) Phylum Rhodophyta
1) Red algae
2) Marine, both shallow and deep
3) Multicellular
4) Chlorophyll a, phycoerythrin: red pigment
5) Reproduction by alternation of generations
6) Economically important: food crop, agar, carageenan (stabilizes paint, ice cream, etc.)
Example: Coralline: Have cellulose cell walls impregnated with calcium carbonate- contribute much to the growth of coral reefs
Lab Examples: Polysiphonia and Porphyra
1) Eukaryotic
a) Greek for "true nucleus"(good kernel).
b) More than 10 micrometers in diameter
c) Elaborate shapes (branch, filamentous, tetrahedral, etc.)
2) Unicellular, multicellular, and colonial.
3) Sexuality evolved with this Kingdom.
4) Ancestors of plants, fungus, and animals.
Transition Between Prokaryotes and Eukaryotes:
Pelomyxa palustris: the only member of Phylum Caryoblastea
1) Single-celled ameboid protist, lives at the bottom of ponds.
2) Nucleus divides more like a prokaryote than a eukaryote.
3) No mitochondria; has bacteria living in it that serve a similar purpose.
Endosymbiotic Bacteria:
1) Live within other cells, perform specific functions for thir host.
2) Endosymbiotic Theory by Lynn Margulis of University of Mass. in the 1960's.
a) Theory states that a critical stage in evolution of the eukaryote cells involved endosymbiotic relationships with prokaryotic organisms (bacteria).
b)Energy-producing bacteria may have come to reside within larger bacteria, eventually evolving into mitochondria (powerhouse).
c) Photosynthetic bacteria may have come to live in association with other larger bacteria, leading to the evolution of chloroplasts- the photosynthetic organelles of plants and algae.
d) Bacteria with flagella may have become symbiotically involved with non-flagellated bacteria, producing larger, motile cells.
Photosynthetic Protists (Algae):
A) Phylum Chlorophyta:
1)Green Algae
-Once incorrectly believed to have given rise to land plants
-Cells of Chlorophyta contain organelles called chloroplasts in which photosynthesis occurs.
-Photosynthetic pigments are chlorophyll a and chlorophyll b and various carotenoids.
-They are the same as those found in plants and are found in similar proportions.
2) Most aquatic- found in fresh and salt water (but not all)
3) Unicellular, filamentous and colonial
-Those that are motile have two apical (tip) or sub-apical flagella.
-Terrestrial algae occurs on moist trunks of trees, moist soil, moist rocks (even on snow).
-Various species are highly specialized, some living exclusively on turtles, green sloths of Costa Rica, or within the gill mantles of marine mollusks.
4) Reproduction in green algae is asexual and sexual: Alternation of Generations
(How things reproduce is a big part of evolution)
a) First phase produces spores - sporophyte (2n, diploid)
b) Second phase produces gametes - gametophyte (1n, haploid)
Lab Examples: Chlamydomonas- has a red eye-spot; Volvox, forms colonies 500-60,000 organisms that act as one unit; Spirogyra and Cladophora- filamentous
B) Phylum Streptophyta (Chara)
Stoneworts (Brittleworts) with calcium carbonate/limestone secretions
(See Figure 30.1, page 582)
1) Precursor to land plants
2) 450 million years old
3) Ancient fossils same as today
4) They are encrusted with white lime
5) Grow several feet tall, slender, threadlike, with whorls of branches a few inches in length
6) Found in fresh water or mildly brackish water (in estuaries)
7) 3 things that make them unique:
a) Unlike most algae which consist of single cells, simple colonies, or chains, stoneworts grow upwards; branches come off of giant central cells.
- giant cells contain many nuclei, are several times the width of a human hair, and an inch or more in length.
b) They have a relatively advanced feature of sexual reproduction which uses eggs and sperm.
c) Their biochemical processes are more similar to land plants than other green algae.
C) Phylum Phaeophyta
1) Brown algae
2) Marine, largest of the algae; kelp. Found worldwide.
-Unique ability to withstand pounding tides due to holdfasts and mucilaginous cell walls.
3) Multicellular
4) Blade: (not a leaf) but leaf like; stipe: resembles a stem; holfasts: resemble roots.
5) Chlorophyll a and c; pigment fucoxanthin (may slow prostate cancer).
6) Reproduction by alternation of generations
7) Economically important: food, fertilizer, iodine, salts, alginic acids (used as an emulsifier in dripless paint, ice cream, pudding mixes, etc.). An emulsifier allows water and oil to mix.
Lab Examples: Fucus and Laminaria
D) Phylum Rhodophyta
1) Red algae
2) Marine, both shallow and deep
3) Multicellular
4) Chlorophyll a, phycoerythrin: red pigment
5) Reproduction by alternation of generations
6) Economically important: food crop, agar, carageenan (stabilizes paint, ice cream, etc.)
Example: Coralline: Have cellulose cell walls impregnated with calcium carbonate- contribute much to the growth of coral reefs
Lab Examples: Polysiphonia and Porphyra
Chapter 28: Prokaryotes
Prokaryotes:
1) Domains Archaea and Bacteria
2) Oldest most abundant form of life
3) Essential
4) Create properties of atmosphere and soil (decomposers).
5) Industrial uses: vinegar, yogurt, cheese, bread, antibiotics
6) Used in mining, ammunition dumps, etc.
Cell Size: Most are 1 micrometer or less in diameter.
General Forms:
1) Bacilli- Rod shaped (bacillus singular)
2) Cocci- spherical (coccus singular)
3) Spirilla- spirally coiled (spirillum singular)
4) Vibrios- short, comma or S-shaped rods (vibrio singular)
Cyanobacteria: Group of photosynthetic bacteria that contain chlorophyll; formerly called blue-green algae, but are not algae, are bacteria.
Cell Interior:
A) Cytoplasm: relatively unstructured, does not have membrane around nucleus or organelles, no mitochondria (powerhouses of the cell). Nucleus instead named nucleoid region.
B) Have ribosomes- smaller and differ in structure than eukaryote cells.
C) Chromosomes in a circular DNA molecule.
D) Plasma membrane is made of different structures in archaebacteria and bacteria (one way to differentiate).
Cell Wall:
A) If the cell wall has a network of peptidoglycan (polysaccharide molecules connected by polypeptide cross links) bacteria is Gram-positive and retains crystal violet stain (purple colored bacteria after staining).
B) If the cell wall has a lipopolysaccharide (carbohydrate chain with lipids) covering the peptidoglycan, the dye will not adhere and it is Gram-negative bacteria.
-Gram Staining helps correlate sensitivity of bacteria to antibiotics.
Flagella and Pili:
A) Flagella made of protein flagellin
- 3-12 micrometers long
- 10-20 micrometers thick
B) Pili shorter than flagella
-Attach cells to substrate
-Also used in conjugation (reproduction).
Endospores:
-Thick wall around chromosome and small portion of cytoplasm.
-Resistant to environmental stress.
-Can revive decades or even centuries later.
-Examples: Tetanus, botulism, anthrax
Motility (Methods):
1) Flagella- rotary (spinning)
2) Gliding- mucous or slime excretion
3) Corkscrew- rotate
Reproduction:
1) Simple binary fission:
-Kingdom Bacteria has ribosomal proteins and RNA polymerase that are different from eukaryotes.
-Kingdom Archaebacteria are very similar to eukaryotes.
2) Two methods of variation:
a) Mutation: million copies in 7 hours (doubling time: 20 minutes)
b) Genetic Recombination: Transfer of genes, usually part of a virus or plasmid or other DNA fragment.
Metabolic Diversity:
1) Autotrophic: Obtain energy from sunlight or inorganic sources. Two types:
a) Photoautotrophic: photosynthetic; contains chlorophyll, but not plastids like plants.
b) Chemoautotrophic: derive energy from inorganic molecules (geothermic vent tube worms, bacteria inside them does this.)
2) Heterotrophic: mostly obtain energy form organic sources. Two types:
a) Photoheterotrophs: obtain energy from sunlight and carbon from other organisms.
b) Chemoheterotrophs: obtain energy and carbon by decomposition (like Rhizobium).
Called saprophytes: obtain enrichment from dead, organic matter.
Different Oxygen Requirements:
1) Aerobes: require oxygen
2) Obligate anaerobes: require no oxygen
3) Facultative anaerobes: can do with or without oxygen
(see page 555, important human bacterial diseases)
1) Domains Archaea and Bacteria
2) Oldest most abundant form of life
3) Essential
4) Create properties of atmosphere and soil (decomposers).
5) Industrial uses: vinegar, yogurt, cheese, bread, antibiotics
6) Used in mining, ammunition dumps, etc.
Cell Size: Most are 1 micrometer or less in diameter.
General Forms:
1) Bacilli- Rod shaped (bacillus singular)
2) Cocci- spherical (coccus singular)
3) Spirilla- spirally coiled (spirillum singular)
4) Vibrios- short, comma or S-shaped rods (vibrio singular)
Cyanobacteria: Group of photosynthetic bacteria that contain chlorophyll; formerly called blue-green algae, but are not algae, are bacteria.
Cell Interior:
A) Cytoplasm: relatively unstructured, does not have membrane around nucleus or organelles, no mitochondria (powerhouses of the cell). Nucleus instead named nucleoid region.
B) Have ribosomes- smaller and differ in structure than eukaryote cells.
C) Chromosomes in a circular DNA molecule.
D) Plasma membrane is made of different structures in archaebacteria and bacteria (one way to differentiate).
Cell Wall:
A) If the cell wall has a network of peptidoglycan (polysaccharide molecules connected by polypeptide cross links) bacteria is Gram-positive and retains crystal violet stain (purple colored bacteria after staining).
B) If the cell wall has a lipopolysaccharide (carbohydrate chain with lipids) covering the peptidoglycan, the dye will not adhere and it is Gram-negative bacteria.
-Gram Staining helps correlate sensitivity of bacteria to antibiotics.
Flagella and Pili:
A) Flagella made of protein flagellin
- 3-12 micrometers long
- 10-20 micrometers thick
B) Pili shorter than flagella
-Attach cells to substrate
-Also used in conjugation (reproduction).
Endospores:
-Thick wall around chromosome and small portion of cytoplasm.
-Resistant to environmental stress.
-Can revive decades or even centuries later.
-Examples: Tetanus, botulism, anthrax
Motility (Methods):
1) Flagella- rotary (spinning)
2) Gliding- mucous or slime excretion
3) Corkscrew- rotate
Reproduction:
1) Simple binary fission:
-Kingdom Bacteria has ribosomal proteins and RNA polymerase that are different from eukaryotes.
-Kingdom Archaebacteria are very similar to eukaryotes.
2) Two methods of variation:
a) Mutation: million copies in 7 hours (doubling time: 20 minutes)
b) Genetic Recombination: Transfer of genes, usually part of a virus or plasmid or other DNA fragment.
Metabolic Diversity:
1) Autotrophic: Obtain energy from sunlight or inorganic sources. Two types:
a) Photoautotrophic: photosynthetic; contains chlorophyll, but not plastids like plants.
b) Chemoautotrophic: derive energy from inorganic molecules (geothermic vent tube worms, bacteria inside them does this.)
2) Heterotrophic: mostly obtain energy form organic sources. Two types:
a) Photoheterotrophs: obtain energy from sunlight and carbon from other organisms.
b) Chemoheterotrophs: obtain energy and carbon by decomposition (like Rhizobium).
Called saprophytes: obtain enrichment from dead, organic matter.
Different Oxygen Requirements:
1) Aerobes: require oxygen
2) Obligate anaerobes: require no oxygen
3) Facultative anaerobes: can do with or without oxygen
(see page 555, important human bacterial diseases)
Chapters 22, 23, 27: Classification, Viruses
Evolution and Taxonomy:
-How new species develop.
-Species: a species is a group of individuals that can interbreed with each other and are reproductively isolated from other such groups.
*The deciding factor is that they only interbreed with each other.
-Like any other area of science, there are exceptions to the rule: some plants, bacteria reproduce asexually.
Two Ways New Species Develop:
1) Allopatric speciation occurs when populations are separated by a geographical barrier that prevents them from reproducing with each other.
a) Variations occur due to different mutations, genetic drift, etc., change from parent type.
2) Sympatric speciation occurs when members of a single population develop a genetic difference that prevents them from reproducing with the parent type. (More common among plants, but also with cichlids in the remote African lake.)
Classification of Organisms:
A. All living organisms have things in common
1) Cells
2) ATP (adenosine triphosphate)
3) Have hereditary material- DNA
4) Evolve
B. Differences Between Organisms (history of classification)
1) The Greeks and Romans started grouping common organisms into genera (genus, singular). Latin for "group."
-Example: Oaks became Quercus (capital first letter, underlined or italicized); cats are Felis.
2) Next the polynomial system evolved
-Scientists used a long string of words to describe the organism (12 or more). This method quickly became cumbersome.
3) Carl Linnaeus started the binomial system in the 1750s.
-Used a two part name for each species
-Standard way of naming organisms used today (always Latin).
-Example: Quercus phellos (Genus, species: Group, kind).
-Escherichia coli, or abbreviated as E. coli.
C. Taxonomy
-The science of classifying living things.
-Hierarchy of groups within groups.
-Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
(Drunk King Phil Came Over For Great Spaghetti!)
Evolutionary Classification:
-Cladogram
1) Based on the order in which species evolved
2) Includes DNA sequencing (is based upon it).
(Review Figure 23.2, pg 456, will be on test)
-Traditional Taxonomy Considers:
1) Key characteristics
2) Uses common descent
3) Amount of adaptive evolutionary change
4) Some bias can come into play because it's a subjective process based on biologists' observation.
5) Historically we did not use DNA sequencing because it simply wasn't available.
(Review also Figure 23.1, pg 454)
3 Domains: Bacteria, Archaea (Prokaryotes), and Eukarya
6 Kingdoms:
1) Archaebacteria (Domain Archaea): Many are anaerobic.
-Three major categories:
a) Methanogens: Use hydrogen gas to reduce carbon dioxide to form methane gas (CH4). Anaerobic, found in swamps, marshes and animals' intestines.
b) Extremophiles: found in extreme conditions of heat, salt, acidic, pressure.
c) Nonextreme: Found in similar conditions as bacteria.
2) Bacteria (Domain Bacteria): Believed to be oldest organism; also most abundant (see page 545). Kingdom Bacteria along with Kingdom Archaebacteria used to be Monera and are prokaryotes.
a) Their cells lack membrane enclosed nucleus and membrane enclosed organelles.
b) They are more metabolically diverse and smaller than eukaryotes.
*The next 4 Kingdoms are eukaryotes:
3) Protista (multi or unicellular)
-Stepping stone from bacteria to everything else.
4) Fungi
5) Plantae
6) Animalia
Viruses
1) Nonliving, simpler than bacteria
2) Acellular
3) Do not metabolize energy, do not have respiration, fermentation, or photosynthesis.
Definition: Nucleic acid encased in a protein coat called a capsid
4) Cannot replicate on their own
5) Uses host to reproduce (parasite)
6) Have DNA or RNA (not both)
7) May be parts of genomes
8) Do not respond to stimuli
(As with everything else in science, there are always a few exceptions)
Examples of viruses: smallpox, chicken pox, shingles, mumps, yellow fever, rabies, aids, flu, polio, some cancers, etc. (Table 21.7, page 527)
Transmissible Spongiform Encephalopathy (TSE's)
-Caused by prions - from protein (proteinaceous infectious particle)
1) Scrapie in sheep
2) Mad Cow Disease in cattle
3) Creutzfeldt-Jakob Disease in humans
4) Chronic Wasting Disease in deer
5) Affects brain and spinal cord by causing Swiss cheese holes
6) No cure
7) Can spread via tissue transplant and food
-How new species develop.
-Species: a species is a group of individuals that can interbreed with each other and are reproductively isolated from other such groups.
*The deciding factor is that they only interbreed with each other.
-Like any other area of science, there are exceptions to the rule: some plants, bacteria reproduce asexually.
Two Ways New Species Develop:
1) Allopatric speciation occurs when populations are separated by a geographical barrier that prevents them from reproducing with each other.
a) Variations occur due to different mutations, genetic drift, etc., change from parent type.
2) Sympatric speciation occurs when members of a single population develop a genetic difference that prevents them from reproducing with the parent type. (More common among plants, but also with cichlids in the remote African lake.)
Classification of Organisms:
A. All living organisms have things in common
1) Cells
2) ATP (adenosine triphosphate)
3) Have hereditary material- DNA
4) Evolve
B. Differences Between Organisms (history of classification)
1) The Greeks and Romans started grouping common organisms into genera (genus, singular). Latin for "group."
-Example: Oaks became Quercus (capital first letter, underlined or italicized); cats are Felis.
2) Next the polynomial system evolved
-Scientists used a long string of words to describe the organism (12 or more). This method quickly became cumbersome.
3) Carl Linnaeus started the binomial system in the 1750s.
-Used a two part name for each species
-Standard way of naming organisms used today (always Latin).
-Example: Quercus phellos (Genus, species: Group, kind).
-Escherichia coli, or abbreviated as E. coli.
C. Taxonomy
-The science of classifying living things.
-Hierarchy of groups within groups.
-Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
(Drunk King Phil Came Over For Great Spaghetti!)
Evolutionary Classification:
-Cladogram
1) Based on the order in which species evolved
2) Includes DNA sequencing (is based upon it).
(Review Figure 23.2, pg 456, will be on test)
-Traditional Taxonomy Considers:
1) Key characteristics
2) Uses common descent
3) Amount of adaptive evolutionary change
4) Some bias can come into play because it's a subjective process based on biologists' observation.
5) Historically we did not use DNA sequencing because it simply wasn't available.
(Review also Figure 23.1, pg 454)
3 Domains: Bacteria, Archaea (Prokaryotes), and Eukarya
6 Kingdoms:
1) Archaebacteria (Domain Archaea): Many are anaerobic.
-Three major categories:
a) Methanogens: Use hydrogen gas to reduce carbon dioxide to form methane gas (CH4). Anaerobic, found in swamps, marshes and animals' intestines.
b) Extremophiles: found in extreme conditions of heat, salt, acidic, pressure.
c) Nonextreme: Found in similar conditions as bacteria.
2) Bacteria (Domain Bacteria): Believed to be oldest organism; also most abundant (see page 545). Kingdom Bacteria along with Kingdom Archaebacteria used to be Monera and are prokaryotes.
a) Their cells lack membrane enclosed nucleus and membrane enclosed organelles.
b) They are more metabolically diverse and smaller than eukaryotes.
*The next 4 Kingdoms are eukaryotes:
3) Protista (multi or unicellular)
-Stepping stone from bacteria to everything else.
4) Fungi
5) Plantae
6) Animalia
Viruses
1) Nonliving, simpler than bacteria
2) Acellular
3) Do not metabolize energy, do not have respiration, fermentation, or photosynthesis.
Definition: Nucleic acid encased in a protein coat called a capsid
4) Cannot replicate on their own
5) Uses host to reproduce (parasite)
6) Have DNA or RNA (not both)
7) May be parts of genomes
8) Do not respond to stimuli
(As with everything else in science, there are always a few exceptions)
Examples of viruses: smallpox, chicken pox, shingles, mumps, yellow fever, rabies, aids, flu, polio, some cancers, etc. (Table 21.7, page 527)
Transmissible Spongiform Encephalopathy (TSE's)
-Caused by prions - from protein (proteinaceous infectious particle)
1) Scrapie in sheep
2) Mad Cow Disease in cattle
3) Creutzfeldt-Jakob Disease in humans
4) Chronic Wasting Disease in deer
5) Affects brain and spinal cord by causing Swiss cheese holes
6) No cure
7) Can spread via tissue transplant and food
Chapters 20-22, Evolution
Evolution:
Science: The word means to know.
Webster's Definition:
1) Systematized knowledge derived from observation and experiments carried on to determine the principles underlying what is being studied.
2) Biology: The science of life, of all living matter and the life processes common to all living things.
Vocab:
-Genotype: Genes of an organism for a particular trait or traits. Ex: BB or Ab
-Phenotype: Visible expression of a genotype. Ex: brown eyes or attached earlobes.
-Allele: An alternative form of a gene (occurs at the same locus on homologous chromosomes).
Evolution During the 19th Century:
1) Lamarck (before Darwin) 1744-1829
-First biologist who really believed in evolution.
-Believed that
a) Descent with modification occurs
b) Organisms adapted to their environment
c) Supported the theory of inheritance of acquired characteristics - Giraffes in Figure 20.1, page 396
-However, experimentation in genetics show us that phenotypic changes acquired during an individual's life are not passed on to its offspring.
2) Charles Darwin
-Hypothesized that common descent occurs and that natural selection results in adaptation to the environment.
-Concluded that adaptation to the environment caused diversification , and this diversification causes the origin of new species.
-Today we say that evolution is descent with modification.
a) The descent of organisms from common ancestors with the development of genetic and phenotypic changes over time that make them more suited to the environment.
*Change is the operative word.
b) If organisms do not change and adapt to the changing environment, they become extinct.
c) Extinction is a big part of evolution, it is normal.
3) The Hardy-Weinberg Principle
-Modern method used to day to tell us what causes evolution.
-Method was developed by G. H. Hardy, an English mathematician, and W. Weinberg, a German physician, early last century.
-Five conditions must be met so that original proportion of the genotype in a population remain constant (a situation that is virtually impossible):
a) No mutation.
b) No gene flow: migration of alleles into or out of the population does not occur.
c) Random mating (by chance); not according to phenotype.
d) Large population with insignificant change in allele frequency - no genetic drift
e) No selection- no selective favors over one genotype than another.
If these conditions are not met, there is evolution.
- Selection
a) Natural selection is the environmental selection of organisms most fit to reproduce, resulting in adaptation.
b) Variations are essential, they make adaptation to the environment possible. Ex: pesticides.
-Mutations during sexual reproduction cause new variations to arise.
4) Evidence for Evolution
-Paleontology- The study of fossils
-Biogeographic Separation
-Comparative Anatomy
-Biochemistry and Molecular Data
A. Fossil:
-any past evidence of an organism that has been preserved in the Earth’s crust.
a) There are intermediate fossils that show intermediate changes, they show a stepping stone in major changes
b) Archaeopteryx: The intermediate between dinosaurs and birds.
B. Biogeography:
- Study of plant and animal distribution on Earth.
-States that related forms evolved in one location then diversified as they continued to spread into other, more accessible areas.
a) Example: Australian continent separated from the other continents about 50 million years ago
b) Marsupials came earlier, placental mammals later.
c) Marsupials have evolved in a different, isolated area as a result of natural selection in relation to similar environments. See Figure 21.18, page 428.
C. Homologous Structures:
a) Structures that are similar because they were inherited from a common ancestor. Not necessarily common function.
-Example: Birds from reptiles: scales changed to feathers.
-Vertebrate forelimbs: same bones, different functions, birds and bats for flight, penguin for swimming, horses for running.
b) Then we have vestigial structures: these are found on current species but are not functional.
-Example: Snakes, loss of legs, but some still have a pelvic girdle, hips with little legs (whales too).
-Humans have a tailbone but no tail.
-Human embryos possess gill slits like a fish and later exhibit a tail.
-We also possess a fine fur (lanugo) during fifth month of development.
c) Analogous structure: different evolutionary origin, similar function.
-Example: Bat wing and butterfly wing.
D. Biochemistry and Molecular Data: (video watched in class)
Science: The word means to know.
Webster's Definition:
1) Systematized knowledge derived from observation and experiments carried on to determine the principles underlying what is being studied.
2) Biology: The science of life, of all living matter and the life processes common to all living things.
Vocab:
-Genotype: Genes of an organism for a particular trait or traits. Ex: BB or Ab
-Phenotype: Visible expression of a genotype. Ex: brown eyes or attached earlobes.
-Allele: An alternative form of a gene (occurs at the same locus on homologous chromosomes).
Evolution During the 19th Century:
1) Lamarck (before Darwin) 1744-1829
-First biologist who really believed in evolution.
-Believed that
a) Descent with modification occurs
b) Organisms adapted to their environment
c) Supported the theory of inheritance of acquired characteristics - Giraffes in Figure 20.1, page 396
-However, experimentation in genetics show us that phenotypic changes acquired during an individual's life are not passed on to its offspring.
2) Charles Darwin
-Hypothesized that common descent occurs and that natural selection results in adaptation to the environment.
-Concluded that adaptation to the environment caused diversification , and this diversification causes the origin of new species.
-Today we say that evolution is descent with modification.
a) The descent of organisms from common ancestors with the development of genetic and phenotypic changes over time that make them more suited to the environment.
*Change is the operative word.
b) If organisms do not change and adapt to the changing environment, they become extinct.
c) Extinction is a big part of evolution, it is normal.
3) The Hardy-Weinberg Principle
-Modern method used to day to tell us what causes evolution.
-Method was developed by G. H. Hardy, an English mathematician, and W. Weinberg, a German physician, early last century.
-Five conditions must be met so that original proportion of the genotype in a population remain constant (a situation that is virtually impossible):
a) No mutation.
b) No gene flow: migration of alleles into or out of the population does not occur.
c) Random mating (by chance); not according to phenotype.
d) Large population with insignificant change in allele frequency - no genetic drift
e) No selection- no selective favors over one genotype than another.
If these conditions are not met, there is evolution.
- Selection
a) Natural selection is the environmental selection of organisms most fit to reproduce, resulting in adaptation.
b) Variations are essential, they make adaptation to the environment possible. Ex: pesticides.
-Mutations during sexual reproduction cause new variations to arise.
4) Evidence for Evolution
-Paleontology- The study of fossils
-Biogeographic Separation
-Comparative Anatomy
-Biochemistry and Molecular Data
A. Fossil:
-any past evidence of an organism that has been preserved in the Earth’s crust.
a) There are intermediate fossils that show intermediate changes, they show a stepping stone in major changes
b) Archaeopteryx: The intermediate between dinosaurs and birds.
B. Biogeography:
- Study of plant and animal distribution on Earth.
-States that related forms evolved in one location then diversified as they continued to spread into other, more accessible areas.
a) Example: Australian continent separated from the other continents about 50 million years ago
b) Marsupials came earlier, placental mammals later.
c) Marsupials have evolved in a different, isolated area as a result of natural selection in relation to similar environments. See Figure 21.18, page 428.
C. Homologous Structures:
a) Structures that are similar because they were inherited from a common ancestor. Not necessarily common function.
-Example: Birds from reptiles: scales changed to feathers.
-Vertebrate forelimbs: same bones, different functions, birds and bats for flight, penguin for swimming, horses for running.
b) Then we have vestigial structures: these are found on current species but are not functional.
-Example: Snakes, loss of legs, but some still have a pelvic girdle, hips with little legs (whales too).
-Humans have a tailbone but no tail.
-Human embryos possess gill slits like a fish and later exhibit a tail.
-We also possess a fine fur (lanugo) during fifth month of development.
c) Analogous structure: different evolutionary origin, similar function.
-Example: Bat wing and butterfly wing.
D. Biochemistry and Molecular Data: (video watched in class)
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