BIL 160- Exam 3

Anatomy of a Leaf Cross Section

From top surface downward: 1. *Cuticle* - a noncellular, waxy sheet of *cutin* secreted by the epidermis 2. *Epidermis* - one-cell thick, lacks chloroplasts. 3. *Pallisade mesophyll*- columnar, photosynthetic (*80% of chloroplasts are located here*) parenchyma 4. *Spongy mesophyll*- cuboid, photosynthetic parenchyma. 5. *Vascular tissue* - xylem on top, phloem on bottom 6. *Lower epidermis* - contains most of the stomates 7. *Lower cuticle* - usually thinner than the upper cuticle

Retained Symbioses (Evidence of Endosymbiosis)

Giardia, a very primitive flagellated protist, contains: 1. Symbiotic, energy-transducing bacteria 2. Two haploid nuclei. (Proof that symbioses happens in nature)

Secondary phloem

Grows outwards, forms a band around the vascular cambium, and lies just beneath the bark. Careless lawn crews working too close with a weed whacker can girdle a tree, severing phloem all the way around. A girdled tree is doomed since it is no longer able to transport organic solutes in water.

Haustoria

Haustoria are specialized, peg-like modified roots that *tap into a host plant's vascular bundles* to extract water, carbohydrates, and nutrients. Parasitic dodders (Cuscuta spp., Convolvulaceae) have little or no chlorophyll, and must feed on a host plant via haustoria.

Sister species (or taxa)

Have already diverged from a common ancestor.

Hawthorne Flies and Apple Maggot Flies (Symaptric speciation)

Hawthorne flies (Rhagoletis pomonella) are native to the U.S. Before European settlers arrived, the flies laid their eggs on hawthorne fruit, which are related to apples. When European settlers brought and planted apples, a subset of R. pomonella began laying eggs on apples. The flies will lay eggs only on fruit type in which they spent their maggothood. Not surprisingly, there is now a R. pomonella population reproducing only on apples. Gene flow between this new population and the original population is highly reduced. Genetic divergence between the incipient species can already be seen.

Transformation vs. Transduction

In *transformation*, the daughter cells aren't identical whereas in *transduction*, they are identical.

Competitive Exclusion Principle (Gause's Law)

In a stable environment, two *species cannot coexist* if they occupy exactly the *same ecological niche.* Species *competing for the same resources must evolutionarily adapt* to exploit different resources, which leads to *resource partitioning.*

Terminal Electron acceptor (Metabolic diversity)

In the Krebs Cycle, the *terminal electron acceptor* can be: 1. *Oxygen* in aerobic bacteria 2. *Nitrate or nitrite* in denitrifying bacteria. These bacteria return nitrogen gas to the atmosphere. 3. *Sulfate* in sulfate-reducing bacteria make stinky H2S as a byproduct. This is the "rotten egg" smell in anaerobic muck. Black H2S will coat your feet black if you sink into anaerobic muck.

Evolution: Gametophyte vs. Sporophyte

In the earliest plants, the *gametophyte* (n) generation was long-lived and dominant. As plants evolved, the gametophyte became more and more reduced. *In most extant plants, the sporophyte is the long-lived, dominant generation (perennial).*

Biological magnification

Increasing concentration of a harmful substance in organisms at higher trophic levels in a food chain or food web

Zoonotic diseases

Infectious diseases of animals that can cause disease when transmitted to humans

Ground tissue (True Tissue Embryophyte Synapomorphy)

Is incorporated into plant infrastructure: 1. *Parenchyma*- thin-walled cells alive at maturity 2. *Collenchyma* - thick-walled cells alive at maturity 3. *Sclerenchyma* - thick-walled cells dead at maturity and is very hard

Photosynthesis

Is the chemical process by which plants and some bacteria 1. Sequester atmospheric carbon dioxide 2. Use it to build carbohydrates. The waste product of photosynthesis is *oxygen*.

Why are plant sex cycles unique?

It changes ploidy, from 2n to n to 2n. So from diploid to haploid to diploid.

John Sutherland

John Sutherland and his team at the University of Manchester, UK demonstrated that RNA nucleotides could have arisen from inorganic precursors by means of a previously unsuspected mechanism. The early oceans were a solution of organic molecules, a "primitive soup" from which life arose *They first "precooked" a sugar and half of a base an intermediate step. Then later on, it may have combined with the other half of the base and a phosphate group to make a ribonucleotide with a cysteine base. They then subjected it to sunlight, and made a ribonucleotide with a uracil base.*

If a group underwent speciation, what should it share with its sister species?

Kingdom Phylum Class Order Family Genus *NOT species*

Heterogamy (Anisogamy) (Embryophyte Synapomorphy)

Land plants are heterogamous and oogamous. Male and female gametes are physically distinguishable and the ovum is large, nutrient-filled, and sedentary while the sperm is small and motile.

Spring Wood

Large vessel lumens develops during spring/early summer since there's lots of water, the lumens become bigger, it looks lighter

LUCA

Last Universal Common Ancestor. The shared ancestor that multiple organisms diverged from

Lecture 11

Lecture 11

Lecture 12

Lecture 12

Lecture 13

Lecture 13

Lecture 14

Lecture 14

Lecture 15

Lecture 15

Corm

Like a bulb, a corm contains: -A basal plate -A thin tunic -A central shoot primordium It lacks visible storage leaves, which distinguishes it from a bulb. Plants that develop from corms include gladiolus, freesias, crocus, and hyacinth.

Zone of Maturation

Location of mature cells that have assumed their final identity

Bisexual/hermaphroditic

Male and female components are *on a single individual and are combined in a single branch/structure.* Called a sphorophyll and the bisexual gametophyte has both an antheridia and archegonia.

Dioecious

Male and female reproductive structures are on *separate individuals.* Megasporophyll (or archegonium) and microsporophyll (or antheridium) are different individuals.

Monoecious

Male and female reproductive structures are on a *single individual, but on different branches.* Megasporophyll (or archegonium) and microsporophyll (or antheridium) are on the same individual but on different branches.

Water Storage Roots

Many plants living in very arid habitats have roots that collect large amounts of water during rainy season. The plant draws on its stores throughout the dry season.

Organelle Genomes (Evidence of Endosymbiosis)

Mitochondria and chloroplast have their own genomes: 1. Largely independent of the nuclear genome (some communication) 2. Chromosome is circular, not linear 3. DNA is not associated histones or RNA. Like prokaryotes, mitochondria and chloroplasts are haploid.

Organelle Structure (Evidence of Endosymbiosis)

Mitochondria and chloroplasts are bounded by two membranes, not one. This may be a remnant of ancient phagocytosis by the original host cell. This is because phagocytosis involved the pinching of the host cell's membrane to make a vesicle.

Organelle Ribosomes (Evidence of Endosymbiosis)

Mitochondria and chloroplasts have their own ribosomes. These are more similar to prokaryotic than to eukaryotic ribosomes.

Mitochondria

Mitochondria are energy-transducing organelles bounded by a double membrane. They are derived from ancient, symbiotic prokaryotes.

Plasmodesmata (Viridiplantae Synapomorphy)

Narrow threads of cytoplasm that pass through pores in the cell walls of adjacent cells which facilitate communication and transport between plant cells.

Neutralism

Neither species benefits or is harmed (0,0).

Is *evolution* and the *Origin of Life* the same thing?

No, evolution is the process by which life changes over time whereas the Origin of Life is how it all started.

When an ancestor diverges, does that mean it's still alive?

No, when it diverges, it becomes extinct since it's split into sister species and no longer resemble the common ancestor. Although one of sister species may still greatly resemble the common ancestor in the node.

Anthropocentrism

Non-human species are important only in so far as they can *benefit humans*. They are important only as resources. Can lead to overexploitation.

Biocentrism

Non-human species have intrinsic value, and should be preserved. *The biocentric view is often subjective.* People with this perspective often focusing preservation efforts on large, charismatic species to the exclusion of less aesthetically appealing species which could be more ecologically important; "Save the whales," save the species that are majestic or beautiful.

Xylem

Nonliving vascular tissue that carries water and dissolved minerals from the roots of a plant *upwards* to its leaves. -*Unidirectional*

Liverworts, Hornworts, Mosses

Nonvascular plants that have a *thallus* and descended from algae; they do NOT have true organs since they lack vascular

Zooxanthellae (dinoflagellates) and coral

One of the most vital symbiotic relationships on earth. Zooxanthellae take up residence inside the corals and gives the coral polyps photosynthetically produced food. Without these dinoflagellates, coral reefs would not exist. Climate change and freshwater runoff causes corals to eject their Zoocanthellae which leads to their demise (*bleaching*).

Obligate mutualism

One species cannot survive without the other (+, +)

Copiotroph

Organisms which thrive in *nutrient-rich* environments, especially those with plenty of carbon.

Can we break α glycosidic or β glycosidic bonds?

Our enzymes are only capable of breaking α glycosidic bonds

Giardia lamblia (Excavates)

Parasitic Giardia lamblia provides a showcase of basal characters. 1. Has typical eukaryotic 9 + 2 flagella 2. Two haploid nuclei 3. Reduced mitochondria (a derived character) 4. No plastids 5. Very simple cytoskeleton 6. Is a *facultative anaerobe* 7. Has no electron transport chain proteins or enzymes associated with aerobic respiration 8. Can cause *giardiasis*- as an intestinal parasite that causes diarrhea

What is bark made of?

Phellem (cork), Phellogen (cork cambium), and Phelloderm (it's just layers of periderm).

The Great Oxygen Catastrophe

Photosynthetic prokaryotes (*cyanobacteria*) that had *chlorophyll a produced oxygen* that seeped into the ocean. As the oxygen accumulated, it reacted with iron in the water to form iron oxide (rust) sediments that sunk. The water then became so saturated with oxygen that some of it bubbled up and was released into the atmosphere. The oxygen that was released wiped out many of the residing living organisms which were anaerobes that couldn't handle deadly oxygen.

Meristem (Embryophyte Synapomorphy)

Plants exhibit *indeterminate growth*: -They produce new tissues throughout their lifetime. The source of new tissues is *meristem*: -Embryonic and totipotent -Can differentiate into any other type of cell

Alternation of Generations (Viridiplantae Synapomorphy)

Plants have more steps to their life cycle than animals do -A *diploid sporophyte* produces *spores* via *meiosis.* -Each *spore* grows into a *haploid gametophyte.* -The *gametophytes* produce *gametes* via *mitosis.* -Sperm and egg join to form a *diploid zygote.* -The *zygote* grows (via *mitosis*) into a *diploid sporophyte.* -Repeat forever

Pneumatophores

Pneumatophores (Greek pneum, "breathe" and phor, "to bear") are aerial roots whose tips are equipped with numerous lenticels. The *root tips protrude from water-logged soil* to provide gas exchange surface.

Lenticels

Pockets of living, unsuberinized parenchyma cells. Gas exchange takes place through these openings in the periderm.

Grass Tolerance to Heavy Metals

Populations of Vernal Sweet Grass, Anthoxanthum odoratum, living around strip mines have undergone selection for tolerance to heavy metals in the soil. -Original population is not tolerant of heavy metals. -Incipient daughter species is tolerant of heavy metals. -Natural selection removes metal-intolerant hybrids from contaminated soil. -Over generations, further divergence is likely to occur. Two ecosystems essentially, one that can only grow on the heavy metal the parent species that cannot.

Secondary Meristems

Procambium gives rises to two secondary (=lateral) meristems or *cambia*: 1. *Vascular cambium* (multipotent): -Located between xylem and phloem -Gives rise to xylem and phloem -*It grows in two direction*, xylem in the inside and phloem on the outside 2. *Cork cambium/Phellogen* (multipotent): -Located between phloem and dermal layer -Gives rise to bark As a tree increases its width (*lateral* growth), the bark formed by the *cork cambium* gets pushes out and cracks

Secondary Xylem

Produces wood toward the interior of the stem (trunk) After several years of growth, the vascular cambium has replaced all primary tissue with secondary growth. 1. *Sapwood* - the outer cortex of a stem where xylem tubes are open and conducting water and minerals coming from the roots 2. *Heartwood* - the central core of a stem where xylem tubes are clogged with resins and no longer conducts water Secondary xylem cell walls contain toxic secondary metabolites that deter herbivory.

Heterotrophs and Autotrophs (Metabolic Diversity)

Prokaryotes can be *heterotrophic* or *autotrophic* 1. Most bacteria are *heterotrophic decomposers.* 2. *Decomposers* break down dead organic matter into its inorganic components. 3. Only bacteria and fungi are capable of this feat. 4. . Cyanobacteria are *photosynthetic producers.* Ancient cyanobacteria initiated production of our oxygen-rich atmosphere. Cyanobacteria can proliferate to cause toxic "blooms" in nutrient-rich water. (autotrophic) 5. Deep Sea Vent Bacteria are *chemosynthetic producers.* They use the intense energy of volcanic deep sea vents to synthesize organic molecules from inorganic components. (autotrophic)

Prop Roots

Prop roots *grow from the lower stem* or trunk and provide *extra support.* They are most commonly seen in plants with relatively flexible, tall stems plants that live in softer soils

Propagative Roots

Propagative roots have meristematic regions from which *new, genetically identical plantlets sprout.* These regions are not the same as axillary buds at stem nodes. They lack a true apical meristem.

What kingdoms are in Eukarya?

Protista, Fungi, Plantae, Animalia

Protist Ecological Roles

Protists are most commonly found in marine and freshwater habitats. They require moisture to survive, but also can live in terrestrial habitats. Various species of protists may be: 1. *Photoautotrophs* (can photosynthesize) 2. *Chemoheterotrophs* -*Predatory*: predator kills prey -*Parasitic*: host is hurt -*Commensal*: host isn't hurt or helped -*Mutualistic*: help both organisms -*Detritivorous*: eat dead organic matter -*Mixotrophic*: can flip back and forth between being a photoautotroph and chemohetertroph

Protist Diversity

Protists... 1. Have descended from multiple different ancestors 2. Are diverse in form and natural history 3. May reproduce asexually and/or sexually, depending on species 4. May be: -*Unicellular* (one-celled) -*Coenocytic* (multiple nuclei in one cytoplasmic mass) -*Aggregate* (clumped together) -*Colonial* (adhered in a more organized form; globe or sphere) -*Truly colonial* (with a cellular division of labor) 5. Protists can vary in size from < 1 μm (Ostreococcus tauri) to > 20cm in diameter (coenocytic Syringammina fragilissima)!

Red Tide

Red tide is a naturally-occurring, higher-than-normal concentration of the microscopic algae Karenia brevis (formerly Gymnodinium breve, a type of *dinoflagellate*). This organism produces a toxin that affects the central nervous system of fish so that they are paralyzed and cannot breathe. As a result, red tide blooms often result in dead fish washing up on Gulf beaches. When red tide algae reproduce in dense concentrations or "blooms," they are visible as discolored patches of ocean water, often reddish in color.

*Heteromorphic* Alternation of Generations

Referring to a condition in the life cycle of plants and certain algae in which the *sporophyte and gametophyte look very different* from one another. It is reflective of the increasingly reduced gametophyte stage that come with more derived plants.

*Isomorphic* Alternation of Generations

Referring to alternating generations in plants and certain *algae* in which the *sporophytes and gametophytes look alike*, although they differ in chromosome number.

Specialized Stems

Rhizomes, Tuber, Tendril, Stolon, Bulb, Corm, Psuedobulb, Cladophyll, Thorn

Rhodophyta (Red Algae) (Plantae)

Rhodophyte synapomorphies: 1. Loss of flagella 2. Loss of centrioles 3. Chloroplasts containing -chlorophyll a -*chlorophyll d* (teally bluey green) 4. Specialized light collecting *phycobilisomes* (protein complex) containing photosynthetic *phycobilin* pigments: -phycoerythrin (red) -phycocyanin (blue-green) -allophycocyanins (blue-green) 5. *Chlorophyll d and the phycobilins are found only in Rhodophytes and cyanobacteria*, evidence of their secondary endosymbiosis. (Note that even though phycocyanin may appear to be blue-green and reflect blue-green light, it can still absorb some blue-green light) 6. Chlorophyll d λmax = 710nm (far red) 7. Phycoerythrin λmax = 495nm (blue) and 545nm (blue-green) 8. Phycocyanins λmax = 621nm (yellow) 9. Absorption of shorter wavelengths allows these algae to live in lower-light conditions than green algae can. 10. Many species of red algae are *coralline*: They deposit *calcium carbonate* in their tissues. The hard, somewhat brittle thallus is a deterrent to herbivory. 11. Agar and Porphyra (seaweed) are both types of rhodophytes

RNA World Hypthesis

Ribonucleic acid (RNA), not deoxyribonucleic acid (DNA),was most likely the original genetic material. -RNA is simpler than DNA to construct from raw materials -RNA has enzymatic properties (*ribozyme* activity) -RNA can modify its own structure -RNA can self-replicate -RNA can be *reverse transcribed* into its more stable cousin, DNA (extant retroviruses demonstrate this process) *Evolution of comparatively stable DNA from an RNA precursor would have conferred a selective advantage on the organisms lucky enough to have synthesized those first DNA molecules. That would be when DNA would take over as the primary genetic material.*

Aerial Roots

Roots that *never touch the ground* & take in moisture from the air. Aerial roots are typically found in epiphytes such as orchids and bromeliads.

Schlerenchyma (Simple Ground Tissue)

Sclerenchyma cells provide compressional strength and support to plant tissues. 1. Sclerenchyma cells lose their living protoplast *(dead) at maturity.* (Parenchyma and collenchyma cells retain their living protoplasts.) -Have *very thick, hard secondary walls* at maturity. -Highly *lignified* 2. Come in two flavors: *Sclerids* -Five different types (some unique to a particular taxon) -May be scattered in other plant tissues. -May be concentrated in specific areas: the "grit" in pear parenchyma/flesh ("stone cells") peach, apricot, cherry, etc. pits nut shells *Fibers* -Are the *main structural support elements* in plants. -Are thin and elongate. -Narrow lumen -Found in many tissues and organs. ~Xylary - found in xylem ~Extraxylary - found in tissue other than xylem -Used by humans to make textiles, paper

Living "Pro-organelles" (Evidence of Endosymbiosis)

Several species of extant cyanobacteria and heterotrophic bacteria have internal membrane systems. These are reminiscent of mitochondrial and chloroplast internal membrane systems.

Which of the following changed a nucleotide bearing cytosine (cytidine monophosphate) into a nucleotide bearing uracil (uridine monophosphate)?

Simulated sunlight

Most of the mass of the carbohydrates plants manufacture during photosynthesis comes from:

Since *carbo*hydrates are made of mostly carbon, it makes sense that it comes from CO2, which comes from the atomosphere

Why did they not have molecular oxygen (O2) in the Miller-Urey apparatus?

Since the oxygen would cause combustion and prevent complex macromolecules from forming. Additionally, it is theorized that Earth's early atmosphere had very little oxygen (*until the Great Oxygen Catastrophe*). Additionally, if there was no life, then photosynthesizing cyanobacteria certainly did not exist.

Summer wood

Smaller vessel lumens develops during late summer since there's less water, it appears darker due to the smaller lumens

What is the lowest level of macroevolution?

Speciation

Endemic species

Species that are native to and found only within a limited area

Coacervates

Spherical droplets that form spontaneously from the association of charged polymers such as proteins, carbohydrates, or nucleic acids surrounded by water

Root Nodules

Swellings consisting of plant cells that contain nitrogen-fixing bacteria

In what type of speciation can a mutation sometimes result in almost instantaneous reproductive isolation, serving as the initial driving force of speciation?

Sympatric speciation

Flagella

The *axoneme* is the central strand of the flagellum (pl. flagella). Visible in cross section are: 1. *Nine peripheral microtubule doublets* 2. *One central microtubule doublet* ("nine surrounding two") A *cilium (pl. cilia)* is a very short flagellum. Its axoneme structure is identical to that of a flagellum. Covered by plasma membrane (unlike bacterial flagellum)

Pollen grain

The *male gametophyte* of a pine or flowering plant is this small, haploid plant.

Secondary endosymbiosis

The *product of primary endosymbiosis is engulfed by a larger cell*, and then takes up residence to the benefit of both cells. Ex. Green algae (which had already undergone primary endosymbiosis by devouring a cyanobacteria) was devoured by a Euglenids.

Anolis spp. (Adaptive Radiation)

The Anolis distichus group in the West Indies share a common ancestor. That ancestral population gave rise and *radiated* into at least 16 different species. Each species is *morphologically adapted to each niche.* Both *sexual selection* and *natural selection* have modified Anolis character.

Hawaiian Honeycreepers (Character displacement, Adaptive Radiation, Resource Partitioning)

The beak trait is the character that is being replaced. 1. An ancestral finch colonized Hawaii millions of years ago. 2. From this ancestor, 51 species of Hawaiian Honeycreepers evolved. 3. Each species is evolutionarily adapted for a *specific foraging strategy.* 4. More than 30% are now extinct (Sadly, 15 since Europeans arrived).

Darwin's Finches (Character displacement, Adaptive Radiation, Resource Partitioning)

The beak trait is the character that is being replaced. 1. An ancestral finch colonized the Galapagos millions of years ago. 2. From this ancestor, 16 different species comprising five genera evolved. 3. The *bill size and shape* of each species reflects a *specific foraging strategy.*

Thallus

The body of a plant-like organism that is not divided into leaves, roots, or stems; undifferentiated into organs, this is a body of a plant or fungus

Late Triassic Extinction (201 mya)

The cause of this extinction is also controversial, but include: -Gradual climate change -Asteroid impact -Massive volcanic eruptions resulting in: 1. The breakup of Pangaea 2. Severe climate changes 3. Ecological disruptions About 30% of marine genera and 42% of all terrestrial tetrapods disappeared. This extinction may have contributed to the rise of the dinosaurs since they were able to fill the niche.

Stele

The central core of the stem and root of a vascular plant, consisting of the vascular tissue (xylem and phloem) and associated supporting tissue.

Domesticated Plants/Animals

The combination of --Few domestic species -Refined by inbreeding ...can set the stage for economic disaster since domesticated animals are *susceptible to disease* due to imbreeding.

Anagenesis (= phyletic evolution)

The conversion of an entire species to a morphologically different form, generating a new species. 1. The evolutionary line does not branch. 2. There is no net increase in species diversity (one species evolves together) 3. The ancestral form gives rise to only one new form. *NOT ACCURATE* The entire population converted from species 1 to species 2 uniformly and then to species 3. All of the species inherit the adaptations automatically.

The Anthropocene Extinction

The current extinction rate has been estimated at 24-150 species lost per day. This is 1,000 times higher than the "normal" extinction rate. The current extinction rate is similar to that of previous mass extinctions. The extinction is *anthropogenic*. 1. Habitat loss 2. Invasive exotic species 3. Pollution 4. Population Explosion 5. Overexploitation

Cladogenesis (= diversifying evolution)

The divergence of an ancestral species/taxon into two sister species/taxa. 1. The evolutionary line branches. 2. There is a net increase in species diversity (sister species) 3. The ancestral form gives rise to two new forms. *Splitting from an ancestor, is more accurate*

Endomembrane System

The endomembrane system defines: endoplasmic reticulum, golgi bodies, vacuoles, lysosomes, peroxisomes, and nuclear envelope.

Biodiversity

The entire array of living organisms found on earth.

Phanaerozoic

The eon encompassing all time, including: -The Cambrian (~540 - 485 mya) -The present time The fossil record contains evidence of at least five past global extinction cycles.

Cytoskeleton

The eukaryotic cytoskeleton consists of 1. *Tubulin*-based microtubules 2. *Actin*-based microfilaments 3. *Various protein*-based intermediate filaments *Is there for structure and transport*

Allopatric speciation/Geographic speciation

The evolution of a *new species* from an ancestral species *due to geographic division* of the ancestral population that prevents gene flow between them; most common mode of speciation

Choanoflagellates (Amorphea)

These stalked, sessile protists may be unicellular, but most are colonial. They are extremely similar to the *choanocytes* found in sponges, the most primitive proto-animals. *Beat their flagellum so that food particles get stuck in the mucus.*

Seedless Tracheophytes Gametophytes

They are small and bisexual and live only for one season (unlike bryophyte gametophytes which are perennial).

Permian-Triassic Extinction (252 mya)

This began after a *series of massive volcanic eruptions* in what is now Siberia. -Lava and ash directly caused die-offs. -Excess CO2 caused global temperatures to rise ~6 degrees F -More uniform temperature across the globe reduced ocean water cycling, reducing oxygen content (ocean anoxia) -Anaerobic bacterial overgrowth in oceans may have increased concentrations of toxic, ozone-destroying hydrogen sulfide (H2S) -Ozone depletion may have contributed to extinctions. Over the course of about 60,000 years, approximately 96% of all animal and plant species died off.

Amorphea

This clade includes the protist groups: 1. *Amoebozoa*-humans are closely related to these and they will eat your brain 2. *Slime Molds*- considered Amoebozoans 3. *Choanoflagellates*-closest related protist group to the animial kingdom; they beat their flagella to acquire food As well as the multicellular Kingdoms: 1. *Fungi* 2. *Animali* Amorphea's monophyly is not certain. But for now....

Archaeplastida (Plantae)

This ecologically vital clade includes: 1. *Rhodophyta* (Red Algae)- chlorophyll d and specialized light collecting *phycobilisomes* (protein complex) containing photosynthetic *phycobilin* pigments: phycoerythrin (red), phycocyanin (blue-green), allophycocyanins (blue-green) 2. *Viridiplantae* (Green Plants)- chlorophyll b A unifying characteristic (*synapomorphy*) is that all plants undergo an *alternation of generations* life cycle.

Cretaceous-Tertiary (K-T) Extinction (65.5 mya)

This event defined the end of the Cretaceous and the beginning of the Tertiary. *This extinction was most likely caused by impact of the Chixulub Comet*, whose crater lies at the bottom of the ocean near Mexico's Yucatan peninsula. About 75% of terrestrial plant and animal species disappeared, including the non-avian dinosaurs. More than half of all marine species also died off.

Why would bacteria produce antibiotics, if antibiotics kill bacteria?

This gives the microbe an advantage when competing for food and water and other limited resources in a particular habitat, as the antibiotic kills off their competition.

Trichonympha and Personympha (Excavates)

Trichonympha and Personympha are *intestinal endosymbionts in termites.* Unlike termites, these protists can digest cellulose. Without them, their termite hosts would starve to death.

Eukaryotes

Unicellular or multicellular organisms made up of cells containing a *membrane-bound nucleus and organelles.*

Polyploidy (Sympatric speciation)

Unlike most animals, plants can generate polyploid zygotes that grow into viable individuals. They can be either defined as a *autopolyploidy* or a *allopolyploidy,* but in both cases, they can no longer reproduce with their parent species due to a *sudden genetic event* that causes isolation, which is known as *sympatric speciation.*

Slime Molds (Amorphea)

We also share a relatively recent common ancestor with *slime molds*, whose phylogenetic relationships are still being determined. Once classified as Fungi, most of these are now believed to be Amoebozoans. Characterized by how they resemble a slime at one point in their life cycle.

Amoebozoa (Amorphea)

We are closely related to *amoebas.* Most specifically, we are most closely related to parasitic *entamoebas.* Don't get this one up your nose. It will eat your brain.

Binary fission (Asexual reproduction)

When a bacterium undergoes binary fission, it replicates its components and then divides into *two identical cells.*

When can you only have organs in plants?

When there's vascular tissue such as xylem and phloem

What is the difference between "brown rot" and "white rot" fungi?

White rot of wood is accomplished by fungi that digest both cellulose and lignin components of wood. Brown rot is accomplished by fungi that digest the cellulose, but leave lignin behind. White rot leaves thready white residual cellulose, whereas brown rot leaves cuboid brown residual lignin.

Workshop 1

Workshop 1

Workshop 2

Workshop 2

Modern systematists follow the rules of the Cladistic System, which states that the only quantifiable feature of evolution is __________________.

cladogenesis

All seed plant gametophytes are _______________. Seed plant gametophytes are so reduced and highly derived that they no longer resemble their liverwort ancestors. But they are completely _____________ to them.

dioecious; homologous

Fossils are ___________ in a clade, just as extant species are.

endpoints (can't say that anything is ancestor of anything with absolute certainty)

The fossil record contains evidence of at least _______ past global extinction cycles

five

Climate and soil conditions determine the _________. ______, in turn influences the _________. *The greater the botanical diversity, the greater the animal diversity.*

flora; flora; fauna

Biodiversity is in constant ______. Species arise and become extinct over time. Global biodiversity on earth waxes and wanes over time, punctuated by _______ _________.

flux; mass extinctions

More than half of animal species are __________, with more than 350,000 described species of beetles

insects

Female

mega-

Male

micro-

Species (and incipient species) evolving from small founder mainland populations arise via __________________ speciation.

peripatric

Why do we have an oxygen-rich atmosphere?

photosynthesis

If something is "sclerified" it will contain significantly more ____________ than an unsclerified structure.

sclerenchyma and lignin

Sporopollenin (Viridiplantae Synapomorphy)

-First seen, evolutionarily, in *Charophyte cell walls.* -Is a major component of land plant *spore and pollen outer walls.* -Is one of the most *chemically inert biological polymers known.* -Is a common component of soils where pollen and spores have dispersed and decayed. -Fossil spores and pollen are well preserved because of the inert nature of the sporopollenin in their outer coats.

Allopolyploidy in a Desert Flower(Gilia, Polemonaceae)

-Gilia minor, Gilia clokeyi and Gilia transmontanaare all native to the Mojave Desert in the southwestern U.S. -Chromosomal analysis reveals that Gilia transmontana is the product of *hybridization* between Gilia minor and Gilia clokeyi. -Gilia transmontana has two sets of chromosomes from each parent species, making it *allotetraploid.* -It is reproductively isolated from its two parent species.

Francesco Redi (1626 - 1697)

-In 1668 this Italian physician experimented by placing rotting meat in covered and uncovered jars. -He noted that maggots *formed only in uncovered jars. And in the mesh-covered jars, the eggs were hatched on top.* -Enlightenment: Maggots are juvenile flies. They come from fly eggs. -Redi is considered by some to be the "Father of Experimental Biology". -*Disproved spontaneous generation with maggots*

Anton van Leewenhoek (1632 - 1723)

-In 1676, this Dutch scientist invented the microscope, revealing a world teeming with microscopic life. -*Interest in spontaneous generation was revived, albeit on a smaller scale.*

Vridiplantae: Green Plants

-Includes all plants, from several taxa of green algae to all land plants. -First green land plants were *green algae* -Green plants have notable *synapomorphies that distinguish them from photosynthetic protists: diverse cell types, chlorophyll b, unique form of starch*

Leaf Modification

-Leaves are highly plastic in form. -The same plant may have leaves of different size, shape, and color, depending on the leaves' growing conditions. -Leaves have undergone more evolutionary diversification and specialization than other plant organs in response to natural selection: 1. Cactus spines 2. Climbing tendrils 3. Prey traps 4. Nutrient storage 5. Water storage 6. Pollinator attraction 7. Drip tips to shed excess rainwater

Root Cross Section

-Like the stem, the root has three main, cylindrical layers.: 1. *Epidermis* (water uptake) 2. *Cortex* (nutrient storage) 3. *Stele* (vascular tissue) -But roots also have two special layers not present in stems: 1. *Endodermis* 2. *Pericycle*- meristematic cells that generate lateral roots and part of the root vascular cambium Another difference between roots and stems: *Stems have nodes, whereas roots do not.* Only stems can sprout side branches from their nodes.

Perennial Woody Plants

-Lives for more than one year -Grows from *primary meristems* -May also have *secondary (lateral) meristems* -May produce both primary (apical merisem) and secondary growth -May or may not become woody -Many types of plants are "woody", but only plants with a *vascular cambium* produce true, botanical *wood.*

Hydrothermal Vents Theory

-Models of ancient membranes are unstable at the high temperatures and salinities near deep sea *hydrothermal *vents, where many suspect life first arose. -But a research team led by *Nick Lane* at University College London discovered that modification of membrane components conferred membrane stability at extreme temperature, pH, and salinity, as are found near hydrothermal vents. Which would cause the formation of *protocells* -Once a stable membrane could form around reacting molecules...the situation was ripe for natural selection.

First Vascular Plants: Just Stems

-Over the next 100 million years, non-vascular ancestors gave rise to vascular plants with: 1. Thicker cell walls 2. Erect stems 3. True tissues, including vascular tissue -*A true plant organ is defined by the presence of vascular tissue.* -Plants with stems appear in the fossil record ~440 mya (Silurian), but molecular data suggest that they were already established ~400mya (Ordovician). -The earliest vascular plants were little more than thin, herbaceous stems. But these early stems gave rise to the fully vascularized true organs: *stem, root and leaf.*

Bacillariophyta (Diatoms) (Stramenophila)

-The *diatoms* have a protoplast encased in a two-part shell composed of silica (glass) -Tiny perforations in the shell allow contact between the cell and its aquatic environment. -The spacing of the holes is so uniform that Swiss watchmakers once used them to calibrate their watches. -*Diatomaceous earth*, the fossilized skeletons of millions of diatoms, is sometimes marketed as a safe insecticide to spread in your carpets to kill fleas: It makes tiny incisions in the exoskeleton that then causes the flea to desiccate. -It is also the *scouring component of "all natural" toothpastes.* -Diatoms are *photoautotrophs* with chloroplasts containing: 1. chlorophyll a 2. chlorophyll c

Sporangium (2n)

-The *sporangium* is a spore (haploid (n) daughter cell)-producing structure. -Inside the "box", many diploid (2n) germline cells undergo *meiosis*. -The resulting *haploid (n)* daughter cells are called *spores*. -Are on *sporophyll*

Stem (First Plant Organ)

-The *stem* is the main body or stalk of a plant. The primitive stem condition is to rise vertically from the ground. -External Anatomy 1. *Apical meristem* - meristem located at the center of a bud 2. *Terminal bud* - growing tip on the end of each shoot 3. *Axillary bud* - growing tip located in each leaf axil 4. *Leaf axil* - the angled space where leaf meets stem 5. *Node* - point on a stem where a leaf is attached 6. *Internode* - stem between the nodes

Isthmus of Panama (Allopatric Speciation)

-The Isthmus of Panama formed 2.8 million years ago, separating the Atlantic and Pacific Oceans and generating the Gulf Stream. -Populations all species living on either side of the isthmus were separated, and proceeded to evolve in isolation from one another. -Example of *allopatric speciation*

Endodermis: A Selective Filter

-The endodermis serves as a "filter" that allows only water and specific molecules into the stele. -This is done by filling intercellular spaces with waxy *suberin.* -Each endodermal cell bears a "belt" of suberin called a *Casparian strip.* -Water and other molecules cannot pass through suberin. -Their only path is through the plasma membrane. -The plasma membrane is highly selective about what it allows through. -Polar substances must pass through very picky membrane channels. -Many non-polar substances can pass through the membrane itself. -Thus, the endodermis filters the solvents and solutes entering the root vascular tissue.

Which of the following is TRUE of both binary fission AND mitosis?

-The process is asexual -The process cannot proceed until DNA is duplicated in the original cell -The process produces two genetically identical daughter cells

Apicomplexa (Alveolata)

-These all-parasitic "*sporozoans*" have a modified Golgi apparatus, the *apicoplast*, at the apex of the cell which facilitates invasion of a host cell. -All apicomplexans are *intracellular parasites of animals*, and are usually host specific. -Some of the diseases they cause include... 1. Babesiosis (Babesia) 2. Malaria (Plasmodium spp.) 3. Cryptosporidiosis (Cryptosporidium parvum) 4. Cyclosporiasis (Cyclospora cayetanensis) 5. Cystoisosporiasis (Cystoisospora belli 6. Toxoplasmosis (Toxoplasma gondii)

Chrysophyceae (Golden Algae) (Stramenophila)

-These are found primarily in fresh water. -Their common name reflects the color produced by *chlorophyll c.* -Prymnesium parvum can cause fish kills when it overgrows, producing a toxin called *prymnesin.* -The toxin generally does not harm animals other than fish. -The calcium carbonate "skeletons" of Emiliana huxleyi, a golden algal haptophyte, are the primary component of the iconic White Cliffs of Dover in England. -Golden Algae are photoautotrophs with chloroplasts containing: 1. chlorophyll a (teal-green) 2. *chlorophyll c* (golden)

Phaeophyceae (Brown Algae) (Stramenophila)

-These marine algae form ecologically important kelp beds that serve as habitat for multitudes of marine organisms. -Floating species such as Sargassum provide habitat for animals in open ocean, where few other resources exist. -The phaeophyte body consists of a: 1. Rootlike *holdfast* to the rocks, doesn't take up rocks 2. Stemlike *stipe* (doesn't have vascular tissues) 3. Leaflike *blade* that does the photosynthesis 4. Gas-filled *floats* that has carbon monoxide that keep it on the surface so it can photosynthesize -Phaeophytes are photoautotrophs with chloroplasts containing: 1. chlorophyll a 2. chlorophyll c 3. *fucoxanthin* (a brownish carotenoid)

Land plants

-They comprise about 98% of earth's biomass. -They are the *main source of our oxygen-rich atmosphere.* -They *fix carbon and nitrogen* into forms other organisms can use. -They are the first link in terrestrial food chains. -They provide habitat and food for all types of organisms *Without plants, life on earth as we know it would not exist.*

Prokaryotic organisms are pre-nuclear.

-They lack a membrane-bounded nucleus. -They lack membrane-bounded organelles. -They have ribosomes and internal membrane systems.

Aleksandr Oparin (1894 - 1980)

-This Russian biologist published *The Origin of Life* (1924) in which he proposed that chemical reactions in the ancient oceans could have generated life. -Later, he studied physical ways that organic molecules might have formed the precursors of life. -Combined gelatin and gum arabica and was able to make *stable globular coacervates.* When lipids were added, these coacervate were able to take up enzymes and substrates and function as a *protocell.*

Edward O. Wilson has estimated that there may be...

...5 - 50 million species of eukaryotes.

Ancestral red algae endosymbiosis gave rise to...

...Dinoflagellates, Apicomplexans ("sporozoans"), Stramenopiles (brown algae and their relatives).

Ancestral green algae endosymbiosis gave rise to...

...Euglenoid, Viridiplantae (Green Plants).

The first genetic material was probably...

...RNA.

Resource partitioning leads species to...

...feed at different times, utilize slightly different prey, develop different physiological adaptations, live in slightly different regions (*character displacement*).

Sporopollenin in aquatic algae allowed plants to colonize land because...

...it protected spores from desiccation and other environmental rigors.

Louis Pasteur (1822 - 1895)

1, In 1862 his elegant Swan-necked flask experiments *convinced the scientific community that microorganisms did not arise via spontaneous generation.* 2. Broth boiled in an open swan-necked flask would stay clear indefinitely. But break off the neck (to remove the curved bacteria trap), and the broth became cloudy with bacteria in a few days. 3. Pasteur's experiments put the controversy to rest. Omne vivum e vivo ("all life from life") became the accepted aphorism.

Different types of speciations:

1. *Allopatric speciation*- geological separation that brings gene flow to a halt 2. *Peripatric speciation*- The daughter species move to an environment where their parents can't interact with them anymore, preventing homogenization 3. *Parapatric speciation*- Graduations until speciation 4. *Sympatric speciation*- No geographic isolation, different species have a mutation or they occupy different niches

The Miller-Urey Apparatus

1. *Apparatus that simulates the conditions of earths ancient atmosphere, oceans, and sources of energy.* It produced organic compounds that are essential for life. 2. They introduced into the apparatus compounds they believed to have comprised the earth's early atmosphere and oceans: carbon dioxide (CO2), water vapor (H20), hydrogen (H2), nitrogen (N2), ammonia (NH3), hydrogen sulfide (H2S), carbon monoxide (CO), methane (CH4) 3. *Samples of water in the apparatus yielded organic molecules that had been formed from the introduced inorganic components.*

Cellulose (Viridiplantae Synapomorphy)

1. *Cellulose* is the most abundant organic molecule on earth. -It is a linear, unbranched polymer of glucose. -Its (β glycosidic) bonds can't be lysed by animal digestive enzymes. -Herbivorous animals require microbial symbionts to digest cellulose (Trichonympha and Personympha (excavuates in termites) -It is crystalline and strong. -It is greyish-white in color. -It is arranged in fibers in the plant cell wall. -This provides *flexible strength* to the cell wall.

Charophyta (Viridiplantae)

1. *Charophytes* are the closest algal relatives of land plants. 2. They share the following synapomorphies with land plants: -Cellulose synthesis occurs in hexameric protein *rosettes*. -Cell walls contain *lignin-like* compounds -*Sporopollenin* present (in Charophyte zygote cell walls) -*Peroxisomes* contain unique, *specialized enzymes* -*Similar flagellated sperm* are unlike those of other green algae -*Phragmoplast* forms near the end of mitosis, creating new cell walls

Specialized Parenchyma

1. *Chlorenchyma* -Is rich in chloroplasts -Is found near the surface of leaves and herbaceous stems 2. *Aerenchyma* -Has large, air-filled intercellular spaces -This can provide flotation (as in water lily leaves). 3. *Transfer cells* -Move substances into other cells via plasmodesmata. -*Companion cells* load substances into vascular tissue for transport. -Provide support and nourishment to vascular tube cells. 4. *Spongy mesophyll* -Facilitates water movement through vascular tissue.

Domain Eukaryote Synapomorphies

1. *Cytoskeleton*- structure and transport with tubulin and actin 2. *Flagella*- structure is different when compared to bacteria flagella 3. *Endomembrane System*- made through *autogeny* 4. *Genome arrangement*- several linear chromosomes and DNA is wrapped around histones 5. *Mitochondria*- came from endosymbiosis 6. *Derived Ribosomes*- 80S ribosomes which are four molecules of RNA complexed with many proteins 7. *Mitosis*- how the reproduce asexually

Male Sexual Prefixes

1. A *microporophyll* develops *microsporangia* that produce male *microspores*. 2. A microspore will grow into a *male gametophyte* (microgametophyte). 3. A male gametophyte has only *antheridia* (synonymous to testes), and produces only *sperm.*

Guard Cells and Stomates

1. A *stomate* is a small opening in the epidermis through which gas exchange takes place. 2. It is bordered by two *guard cells*. 3. In vascular plants, the guard cells can change shape with turgor pressure. -*Turgid* guard cells *open* the stomate -*Flaccid* guard cells *close* the stomate

Female Gametophyte (n)

1. A female gametophyte (n) is also known as a *megagametophyte.* 2. Megagametophytes have female sex organs called *archegonia.* 3. Each archegonium produces *one haploid ovum*. 4. Although they are haploid, archegonia can be considered *analogous to ovaries.*

Bisexual Sexual Prefixes

1. A generic *sporophyll* develops plain old *sporangia* that produce plain old *spores.* 2. A spore will grow into a *bisexual gametophyte.* 3. A bisexual gametophyte has *both antheridia and archegonia.*

Male Gametophyte (n)

1. A male gametophyte (n) is also known as a *microgametophyte.* 2. Microgametophytes have male sex organs called *antheridia.* 3. Each antheridium produces many haploid *sperm*. 4. Although they are haploid, antheridia can be considered *analogous to testes.*

Central Vacuole (Viridiplantae Synapomorphy)

1. A typical plant cell contains a large, single central *vacuole.* 2. It can occupy 80% or more of the cell's internal volume. 3. The vacuole -Stores water -Maintains cellular *turgor pressure* -Shrinks and grows with water availability 4. The water-filled vacuole pushes the cytoplasm and its contents--notably the chloroplasts--outwards. 5. *The vacuole positions the chloroplasts closer to incoming light, making more energy available for photosynthesis.*

Green Algae (Viridiplantae)

1. About 4300 green plant species are unicellular or multicellular *green algae.* 2. Because they *lack vascular tissues* (which defines true plant organs) they do not have true stems, roots, or leaves, although some species have structural analogies (thallus): -*Stipe* ("stem") -*Holdfast* ("root") -*Blade* ("leaf") 3. Many species tend exhibit multicellularity via: -*Aggregates* and *colonies* -*Coenocytic* thallus (multinucleate body with no cell walls; one big cell) -True *multicellular* thallus

Annual Herbaceous Plants

1. All plants begin their development as *herbaceous* (non-woody) sprouts. 2. *Herbaceous* plants are pliable, having little or no lignin. 3. *Woody* plants develop lignified stems and roots, becoming rigid with maturity. 4. An *annual* plant: -Lives, reproduces, and dies in about a year -Grows only from -Primary *meristems* -Produces only *primary growth* -Remains *herbaceous*

Alveolata (SAR Clade)

1. Alveolates share a distinct synapomorphy: sac-like *alveoli* under the plasma membrane. These small vesicles form a *pellicle* that maintains the cell's shape. 2. Various parts of the pellicle may be flexible and contractile or quite rigid. 3. Alveolates include some of the most complex of all protists. Includes: -*Dinoflagellates* are responsible for *red tides* and have a symbiotic relationship (zooxanthellae) and *coral* -*Apicomplexa* are parasitic "sporozoans" with an *apicoplast* and are host specific -*Ciliophora (ciliates)* are covered in *cilia* and have a micronucleus for reproduction and a macronucleus for regulation. They are the most diverse protist group.

Apical meristem

1. Found at the tip of every root and shoot and it is produces new cells, it increases in length (*primary growth). 2. Mature into *three primary meristems*- *protoderm* (epidermis), *procambium* (vascular), *ground meristem* (ground) 3. Called the *Zone of Cell division* where one daughter cell remains meristematic and begins a path of differentiation.

Meristem Tissue

1. Found mainly at the tips of the roots and shoots, where it can produce new cells for growth; It exhibit *indeterminate growth* and is totipotent 2. Can be: apical, intercalary, and lateral meristems 3. Comprise of Zone of Cell Division (apical meristem) and Zone of Elongation (primary meristems) 4. *Primary Meristems*: protoderm, procambium, ground meristem 5. *Secondary meristems* come from the primary meristem procambium: *vascular cambium and cork cambium (phellogen)*

Viridiplantae (Plantae/Archaeplastida)

1. The *Green Plants* form a diverse assemblage ranging in complexity from unicellular Chlamydomonas to giant Sequoia trees. 2. Like all photoautotrophs, they use *chlorophyll a* as their primary electron acceptor. 3. But they share a number of synapomorphies unique to green plants, including: -Energy stored as *starch inside plastids* -*Chlorophyll b* (unique to Viridiplantae)

Thermophiles

1. Thermophiles thrive in *extremely hot environments.* 2. They are found in -Sulfur hot springs -Deep sea thermal vents 3. *The closest living relatives of Eukaryotes are thermophile archaeans.* 4. New research from the laboratory of Nick Lane at University College London provides evidence that *deep sea vents could have provided a biochemical environment conducive to forming protocells,* a necessary step in the origin of life. 5. *Thermal vent protocells may have given rise to the first thermophilic archaeans.*

All ancestors are hypothetical because:

1. They are dead and gone 2. They cannot be directly observed 3. Ancestor status cannot be assigned to a particular fossil with any degree of certainty.

Lazaro Spallanzani (1729 - 1799)

1. This Italian priest suspected that microorganisms had entered Needham's flask after boiling. 2. In 1768, Spallanzani -Filled two flasks with broth -Sealed one, but not the other -Removed the air from the sealed flask, creating a partial vacuum -Boiled broth in both flasks -*Only the unsealed flask produced microorganisms.* However, his experiments were discounted because -Others with less meticulous techniques could not replicate his result. -Critics claimed he showed only that air was necessary for spontaneous generation.

Rhizaria (SAR Clade)

1. This clade includes related shelled and unshelled *amoebas* that bear long, threadlink *pseudopods.* 2. Includes: -*Foraminifera* have calcium carbonate shells and the pseudopods emerges from holes in the shell -*Radiolaria* have shells of silica and also have holes in their shells for their pseudopods

Halophiles

1. Thrive in *extremely salty environments* and grow profusely in evaporation pond sand very salty water (e.g., Great Salt Lake). 2. They are stinky 3. They owe their salt tolerance to: -*High lipid content* of the plasma membrane -*Protective gel capsule* outside the membrane -*High internal salt concentration* (minimizes osmosis)

Transduction

1. Transduction is the acquisition of foreign bacterial DNA by means of a *viral intermediate* that is called a bacteriophage. 2. Transduction involves the acquisition of new genetic material. 3. *A transduced bacterium yields identical daughter cells via fission.*

Transformation

1. Transformation is genetic recombination via uptake of bacterial genes from the *environment*. 2. Transformation *involves the acquisition of new genetic material.* 3. A transformed bacterium yields *non-identical daughter cells* when it undergoes fission- one daughter cell has is identical to the parent and the other one isn't and has the new genetic information

The Origin of Eukaryotes

1. Two processes contributed to the origin of eukaryotic cells. 2. Each occurred more than once in our evolutionary history. 3. *Autogeny*: The external membrane kept on pinching itself until a complex network of membranes were made 4. *Endosymbiosis*: First proposed by *Lynn Margulis*, this model describes how small, energy-transducing prokaryotes: -Were ingested as prey, but not digested -Took up residence as internal symbionts *Eventually, host and internal resident became inextricably linked in a mutually beneficial symbiotic relationship.*

Life on earth originated at least ____________________________. It has been diversifying and expanding ever since.

4 billion years ago

How many species on earth are there?

50 - 500 million

Pilus

A *specialized*, tubular *fimbria* that is used during *conjugation* to transfer DNA from a *donor bacterium* to a *recipient bacterium.*

Types of Plants

A *xerophyte* is adapted for life in a very arid environment. A *hydrophyte* is adapted for life in a very wet environment. A *mesophyte* is adapted for life in a moderate environments.

Sporophyll (2n)

A 2n diploid modified leaf that bears *sporangia* and hence is specialized for reproduction.

Lawn

A bacterial colony that has grown to form a field or mat

Bulb

A bulb is an *underground stem consisting of a dense basal plate (short stem axis) shoot primordium...enclosed by thick, fleshy leaves.* In some cases, the leaves function as nutrient storage reservoirs during dormancy. Old leaves dry and form a protective tunic around the fleshy, nutrient storage leaves. One particular bulb plant will be so familiar to you, it will make you cry.

Cladophyll

A cladophyll is a flattened stem that serves the photosynthetic function of a leaf.

Mature *Herbaceous* Stem (cs)

A cross section of an herbaceous stem reveals a somewhat more complex structure. 1. *Epidermis*- the "skin" 2. *Cortex* - ground tissue infrastructure: -Mostly parenchyma -May be fortified with collenchyma and some sclerenchyma 3. *Vascular bundles/fascicles*: ~Phloem: transports organic solutes in water ~Xylem: transports inorganic solutes and minerals in water 4. *Pith* - composed of parenchyma There is no vascular cambium if this plant remains herbaceous throughout its lifespan.

Tracheophyte

A derived *vascular plant* where *sporophyte (2n) is the *dominant* life cycle stage and *gametophyte* (n) is small and *ephemeral/seasonal.*

Ursus spp. (bears) (Peripatric Speciation)

Polar bears (Ursus maritimus) and Brown bears (Ursus maritimus) share a common ancestor with the extinct Eurasian Brown Bear (Ursus arctos) that once lived in Europe. As the ancestors of polar bears dispersed northward from their original range, glaciation may have made movement southward difficult, isolating them from the more southern populations. Contributing to speciation: genetic drift new mutations reduced gene flow new selective pressures As climate change allows Brown Bears to disperse farther north, hybridization has been documented between Brown and Polar Bears :(

*Allo*polyploidy

Polyploidy resulting from contribution of chromosomes from *two or more species.*

Tendril

A tendril is a *stem modified for clinging and climbing.* (Tendrils also can be modified leaves.) Tendrils are *positively thigmotropic*: they grow towards areas of physical contact.

Thorn

A thorn is a *sharp, protective modified stem.* Not all plant poky-bits are stems. They also can be derived from -Sclerified, pointed epidermis ("prickle") -Sclerified, pointed leaf ("spine") -Sclerified, pointed trichome ("bristle") Thorns and spines have vascular tissue traces. Prickles do not.

Fimbriae

A threadlike extension from the bacterial surface.

What is the gametophyte in the angiosperms, the most derived plants?

A tiny blob of cells deep inside the flower's ovary that's only job is to make gametes.

Tuber

A tuber is a *rhizome modified to store nutrients and starch.* The most familiar example is a potato, but wild tubers have been an important food source for hunter-gatherer humans for thousands of years.

Parasitoidism

A type of parasitism in which an insect lays eggs on or in a living host; the larvae then feed on the body of the host, eventually killing it.

Adventitious Roots

Adventitious Roots *arise from a non-root organ (stem or leaf).* Adventitious roots may be produced either: -During normal development -In response to stress conditions: flooding, nutrient deprivation, wounding

Sequential endosymbiosis

After the first eukaryotic cells had formed, additional endosymbioses led to further divergence of eukaryotic lineages.

Bacteriocidal

Agent that *kills* bacteria

Chloroplast

All plants have similar *chloroplasts*: 1. Enclosed by a *double membrane* 2. Photopigments are embedded in internal *thylakoid* membranes 3. Thylakoids are arranged in stacks called *grana* 4. Grana are connected by a membrane channel system 5. Colorless, aqueous *stroma* forms the fluid matrix around the grana 6. The chloroplast is the site of *photosynthesis*, the biochemical reaction that allows life on earth (as we know it) to exist.

What kind of speciation is *continental drift* an example of?

Allopatric speciation since as they split, the species residing in each land mass subjected to different mutations, climate, natural selection which led to their evolution and subsequent speciation.

Invasive exotic species

An *exotic species* that aggressively *displaces native species*.

Ruminants

An animal, such as a cow or sheep, with an elaborate, multi-compartmentalized stomach specialized for an herbivorous diet. *Methanogens* are symbiotic with ruminant; cow fart and belch methane, which contribute to global warming.

Adaptive Radiation

An evolutionary pattern in which many species evolve (radiate) from a single ancestral species Can be driven by: 1. Mutation 2. Migration 3. Assortative mating 4. Genetic isolation 5. Natural selection

*Auto*polyploidy

An individual has more than two sets of chromosomes, both of which from the *same parental species* (meiosis gone bad).

Suberin

An inert impermeable waxy substance secreted by phellem cells into their walls before they die; its impermeability is solved by *lenticels.*

Predation

An interaction in which one organism kills another for food.

Oligotroph

An organism that grows best at very *nutrient rich* concentrations

Respiration (Metabolic diversity)

Any organism can be of three basic types regarding oxygen tolerance/metabolism: 1. An *obligate anaerobe* can perform only fermentation. It is killed by oxygen. 2. An *obligate aerobe* performs primarily aerobic metabolism. It cannot survive long without oxygen. 3. A* facultative anaerobe* can do either aerobic respiration or fermentation, depending on environmental conditions. Bacteria come in all three flavors, depending on species

If the Woese's cladogram is correct, which two taxa share the most recent common ancestor?

Archaea and Eukarya

Extremophiles

Archaea that live in extreme environments.

Domain Eukarya is more related to ____________ than to _____________.

Archaea; Bacteria

Parenchyma (Simple Ground Tissue)

Are the most abundant plant cells -Are found in most tissues of land plants. -Are spherical alone, but multi-sided when squashed together. -(Most have 14 sides!) -Have a large central vacuole have *thin, flexible walls* -Store starch grains, oils, and other plant products -*Form most of the soft/crispy plant parts (edible)* -Can divide and multiply long after they are mature. -Have long lifespans. Some can reach 100 years of age!

Late Ordivician Extinction

Biodiversity expanded tremendously in the Ordovician's *relatively mild climate.* The northern hemisphere was mostly ocean, with shallow water conducive to life. The Ordovician (485 - 444 mya) fossil record reveals a rich marine invertebrate fauna, early fish, and macroalgae. By the late Ordovician, Gondwanaland (the largest land mass) occupied the south pole. *Massive glaciation and sea level drop caused shallow seas to dry up, with devastating ecological effects.* About 60% of all marine invertebrate genera and 25% of all marine invertebrate families went extinct.

Detritivorous vs. Decomposers

Both eat *dead organic matter*, but detritivorous organisms poop out organic matter whereas decomposers break them down into their inorganic components

Organelle Reproduction (Evidence of Endosymbiosis)

Both mitochondria and chloroplasts undergo fission to reproduce themselves. The process is similar to bacterial fission. Mitochondria reproduce independently of other organelles.

Buttress Roots

Buttress roots are *wall-like extensions from the base of the trunk*. They provide support against physical assault from high winds exerting force on the canopy.

Lichen

Formed by the symbiosis of a fungus and an autotroph, lichens absorb nutrients directly from the air. They cannot tolerate air pollution, particularly sulfates and nitrates, which react with water in their tissues to become strong acids. *Presence of lichen is an indication of good air quality.*

Dermal tissue (True Tissue Embryophyte Synapomorphy)

Forms *epidermis* in herbaceous plants and forms *bark* and associated structures in woody plants

Radioaria (Rhizaria)

These aquatic amoebas secrete shells of *silica (glass)*. Threadlike pseudopods protrude from holes in the shell.

Kingdom Viridiplantae Synapomorphies

(Are a part of the clade Archaepl astida/Plantae) 1. Diverse cell types 2. *Chlorophyll b*- emerald color 3. Unique form of starch- *amylopectin, amylose, cellulose* types & functions) 4. Rigid, layered *cell wall* (cellulose, hemicellulose, lignin, pectin) 5. *Plasmodesmata* (intercellular contact/communication) 6. Large, central *vacuole*(s) (structural support, storage) 7. *Plastids* (various types and functions) 8. *Sporopollenin*- component of spore and pollen outer walls; very resilient 9. *Alternation of Generation*- switch between sporophyte and gametophytes

Excavates

(Clade of Protists) 1. Are characterized by a groove "excavated" on one side of the cell 2. *Giardia lamblia*- reduced mitochondria and facultative anaerobe, causes giardiasis 3. *Trichomonas vaginalis*- most common protist pathogen 4. *Trichonympha and Personympha*- termites have a mutualistic relationship with them to break down cellulose 5. *Euglenozoans*- mixotroph that is neither a plant or animal 6. *Kinetoplastids*- causes serious parasitic diseases

Multiple, Competing *Hypotheses* on the Origin of Life

*Conventional Wisdom*: Earth's primordial atmosphere was reducing, and thus conducive to formation of complex molecules. *Alternative Hypothesis*: Earth's early atmosphere was only weakly reducing, or even neutral. *Alternative Hypothesis*: Earth's early atmosphere was rich in either CO2 or H2 (also conducive to complex organic molecule formation) *Alternative Hypothesis*: Life may have its origin in places other than earth's surface, such as: -Deep sea thermal vents -Space debris collisions with earth

Ecocentric view

*Ecosystems and the biodiversity comprising them should be preserved.* The working whole is more important than any single component. Disassembling an ecosystem can be likened to disassembling a human body. The ecosystem is greater than the sum of its parts.

Koch's Postulates

*In order for a microbe to be confirmed as the cause of a disease, these four conditions must be met.* *1.* The suspected pathogen must be found in all individuals suffering from the disease. *2.* The pathogen must be isolated from the diseased host and grown in pure culture. *3.* The pathogen from the pure culture must cause the disease when it is introduced into a healthy but susceptible host. *4.* The pathogen must be isolated from the inoculated animal and positively identified as the original pathogen.

Bacteriostatic

*Inhibits* bacterial growth

Relationship between Pathogens and Gram Staining

*Pathogens* are often gram negative since they usually have a gel capsule that prevents the staining. This gel capsule is useful for a pathogen since it protects the bacteria from the host immune system and peptidoglycan-targeting antibiotics.

Phloem

*Phloem* conducts water and organic substances in different directions (*multidirectional*) through: 1. *Sieve tube elements* -Contain a living protoplast -*Lack organelles or nucleus* (so water and flow through unhindered) -Relatively wide lumen lie end-to-end to form *sieve tubes* 2. Companion cell -Is a type of transfer cell (specialized parenchyma) -Is paired with a single sieve tube element (its sister cell) -Living cell with all organelles and nucleus -Provides metabolic support to its partner sieve tube -Loads photosynthetically produced molecules into phloem

Leaf Arrangement/Phyllotaxy

*Phyllotaxy* is the arrangement of leaves along the length of the stem at the nodes. 1. *Opposite* - Two leaves per node -Offset in opposite directions 2. *Alternate* -One leaf per node --Offset in alternating directions 3. *Whorled* -Multiple leaves per node -Attached in a radial pattern. 4. *Helical* -One leaf per node --Each offset to form a helical pattern

Plasmids vs. Plastids

*Plasmids* are small, circular of autonomously replicating DNA (refers to bacterias), while *plastids* are a class of small organelles, such as chloroplasts, in the cytoplasm of plant cells, containing pigment or food.

Aggregate Bacteria

*Staphyl-*: clustering bacteria *Strept-* link forming bacteria

What did the Russian chemist A. I. *Oparin* and British scientist J. B. S. Haldane independently hypothesize?

*That Earth's early atmosphere was a reducing (electron-adding) environment, in which organic compounds could have formed from simpler molecules.* The energy for this synthesis could have come from lightning and UV radiation. Haldane suggested that the early oceans were a solution of organic molecules, a "primitive soup" from which life arose.

Trichomonas vaginalis (Excavates)

*Trichomonas vaginalis* is another opportunistic parasite/pathogen. It shares many primitive characters with Giardia. *It is the most common protist pathogen in humans in industrialized countries.* Its name comes from the location where it was first discovered, but it shows up elsewhere, too.

Bacteria as Pathogens

-A *pathogen* is a disease-causing agent. -The vast majority of bacteria are non-pathogenic or beneficial. -However, many can cause disease in plants and animals. -Many bacterial species are ubiquitous and usually do not cause disease. -However, in an *immunocompromised* animal, they can proliferate. Many common bacteria can become *opportunistic pathogens*, given a suitable environment.

Poison Dart Frogs (Adaptive Radiation)

-A single species, the Strawberry Poison Dart Frog (Dendrobates pumilio) exhibits different color morphs in different regions of Panama. -The more brightly colored the frog, the more toxic it is. -Females significantly prefer individuals of their own color morph (*assortative mating*) -This reinforces the ecological signal that warns predators of toxicity.

Georges Buffon (1707 - 1788)

-Curator of the King's Garden in Paris, this intellectual was the first European to propose that the earth and solar system had arisen due to natural processes. -He noted that the earth and living things were all composed of the same types of "particles" (elements). -Although he did not propose a mechanism for life's emergence, he was *among the first to propose an idea other than divine creation.*

Three Domain System

-Domains Bacteria, Archae, and Eukarya. -Developed by *Carl Woese* in 1977 -Based on *synapomorphic rRNA sequences.* since RNA is highly conserved -Inspired *RNA World Hypothesis* where RNA was the first nucleic acid to evolve.

Extinction

-Endpoint for evolution. -It is a natural process. -Most species that ever existed on earth are now extinct.

Domain Archaea

1. *Earliest life form*, spent first 2 billion years as the only life form 2. Archaeans share *some similarities with bacteria*: -They have one circular DNA chromosome -They are *haploid.* -They reproduce via *binary fission* (asexual) -Their shapes can be superficially similar to those of bacteria 3. The archaean genome ranges widely in size among different species.It may be anywhere from ~500,000 - 6,000,000 bp (base pairs) long. 4. *Archaean synapomorphies* -A cell wall composed of material unique to Archaeans -Flagella composed *flagellin* proteins *unique to Archaeans* -Unique tRNAs -Cell membrane structure/composition unique to Archaeans -*Ribosomes more similar to eukaryote ribosomes than to bacterial ribosomes* 5. *Extremophiles*- very hot and salty and oxygen deficit environments 5. Can be *halophiles (salty), methanogens (anaerobic), thermophiles (extremely hot).*

The Value of Biodiversity

1. *Genetic diversity* 2. *Natural biological control of pest species*- Herbivores reproduce faster then carnivores; pesticides remove both helpful and harmful species 3. *Source of food and natural products* 4. *Ecological processes that protect and sustain us* -Water quality: Areas that have forest areas have better water quality then ecosystems without forest areas provided by forests -Pollination 5. *Enjoyment of aesthetic beauty*-green calms us down 6. *Scientific interest* 7. *Complex ecosystems (diverse) protect their component species* 8. *Unknown future benefits*

Mechanisms that drive speciations can be :

1. *Geographical*- physical barriers 2. *Ecological*- use different resources; different niches 3. *Genetic*- mutations

Gram staining

1. *Gram Positive (G+)*: -Bacteria thick peptidoglycan layer -Stains dark *purple* with *gram stain* 2. *Gram Negative (G-)*: -Thinner peptidoglycan layer -Lies between inner and outer plasma membranes -*Does not stain* dark purple with *gram* stain -Stains *pink with safranin* counterstain

Three types of Archaea (Extemophiles)

1. *Halophiles*-extremely salty 2. *Methanogens*- anaerobic 3. *Thermophiles*- extremely hot

Lignins (Viridiplantae Synapomorphy)

1. *Lignins* are the second most abundant of all organic molecules. 2. Lignins... -Are complex organic polymers with variable functional groups. -Fortify land plant cell walls (and those of some green algae) -Are particularly *abundant in wood*y plants -Provide rigid, *compressional strength* to cell walls -Are nearly indestructible -Vary in composition among plant species -Are waterproof, and so help direct water through xylem tubes -Are reddish-brown in color -Have significant *anti-microbial properties* 3. Lignins may originally have evolved to serve as *microbe inhibitors.* Only later were they conscripted for structural uses. 4. *Toxic aromatic compounds* released into the air by wood and other biomass burning and into rivers from paper mills contain lignins and their chemical byproducts.

Plant Tissues

1. *Meristem*- totipotent cells -*Apical*- Increase plant length which is primary growth -*Lateral*-Increase plant girth (side ways) which is secondary growth and derived from primary meristems that come from apical meristem -*Intercalary*- increase plant length 2. *Simple tissues*- one cell type (simple ground tissue) -Parenchyma -Collenchyma -Sclernchyma 3. *Complex tissues*- composed of more than one type of cell Dermal Tissues -Epidermis -Periderm Vascular Tissue -Xylem -Phloem

Nitrogen Cycle

1. *Nitrogen fixation* is conversion of atmospheric nitrogen to nitrogen compounds plants can take up and assimilate. 2. *Nitrogen fixation can be performed only by bacteria*: -Free living cyanobacteria and a few genera of heterotrophic bacteria -Mutualistic Rhizobium bacteria living in legume root nodules 3. Denitrification is the decomposition of nitrate-->nitrite-->ammonia-->N2 4. *Denitrification* can be performed only by a few genera of bacteria: -Nitrosomonas spp. - convert ammonia to nitrite -Pseudomonas spp. - convert nitrite or nitrate into N2 (denitrification)

Epidermis Cell Types

1. *Pavement cell*- the main epidermal cells are thin and flattened 2. *Guard cells*- border the stomates 3. *Trichomes*- bear hairlike extensions; can deliver toxins; can confer *pubescence* ("hair") All of these cells lack chloroplasts.

Cell Wall Layers

1. *Primary cell wall*: relatively thin and flexible made of cellulose, hemicellulose, and pectin. 2. *Middle lamella*: thin gelatinous layer between primary walls of adjacent cells that is primarily composed of pectins and acts like a glue. 3. *Secondary cell wall* (in some cells): added between the plasma membrane and the primary cell wall that is made of cellulose, hemicellulose, lignin (not all cells), waxy *suberin* and *cutin* (not all cells).

Evidence of Endosymbiosis

1. *Retained Symbiosis* - Giardia contains a symbiotic, transducing bateria and two haploid nuclei (proof that symbiosis can happen) 2. *Living "Pro-organelles"*- some bacteria looks like mitochondria and chloroplasts 3. *Organelle structure*- mitochondria and chloroplasts have two membranes which may have from the pinching of the membrane in phagocytosis 4. *Organelle reproduction*- mitochondria and chloroplasts independently undergo fission to reproduce themselves 5. *Organelle Ribosomes*- mitochondrion and chloroplasts have their ribosomes which are more similar to prokaryotes 5. *Organelle Genomes*- have their own circular DNA that lacks histones or RNA, they are also haploid

Root Epidermis (Water Uptake)

1. *Root epidermis( is the surface that meets the environment. It is the first barrier encountered by fluids entering the root from the soil. 2. Surface area is increased by *trichomes* that form *root hairs.* 3. *Root hairs are found primarily in the Region of Maturation. They die off as the cells age.* 4. *Thus, most water enters the root very close to the root tip.* 5. Although epidermal cell walls contain waxy *suberin*, water and minerals can pass easily between the cells of the epidermis. 6. Most filtration is performed by the endodermis.

Spore (n)

1. *Spores (n)* are the *propagules* (agent of reproduction) produced by the sporophyte. 2. The sporangium breaks open to release mature spores. 3. A lucky spore will land on a moist, hospitable spot. 4. The spore will *germinate* and grow via *mitosis* into a *gametophyte.*

Female Sexual Prefixes

1. A *megasporophyll* develops *megasporangia* that produce female *megaspores.* 2. A *megaspore *will grow into a *female gametophyte* (megagametophyte). 3. A female gametophyte has only *archegonia* (synonymous with ovaries), and produces only *ova.*

Specialized Roots

1. Food Storage Roots 2. Water Storage Roots 3. Adventitious Roots 4. Propagative Roots 5. Pneumatophores 6. Prop Roots 7. Aerial Roots 8. Buttress Roots 9. Contractile Roots 10. Haustoria

Secondary Metabolites (Embryophyte Synapomorphy)

1. An organism produces *primary metabolites* necessary for normal growth, development, or reproduction. 2. A *secondary metabolite* is an organic compound not directly involved in an organism's normal growth, development, or reproduction of the organism. 3. *Secondary metabolites are derived from primary metabolites* which may be components of *nectars, fragrances, toxins, herbivore deterrents, etc.* Ex. -Alkaloids -Amines -Cyanogenic -Glycosides -Aromatic scent -Compounds -Terpenes -Steroids -Flavonoids -Non-protein amino acids -Lectins -Phenolic compounds -Tannins -Waxes

Criteria To Be Alive

1. An organized structure (*anatomy*) 2. Chemical reactions coordinated to perform vital functions (*metabolism*) 3. Ability to maintain constant internal environment (*homeostasis*) 4. Reactions internal and external stimuli (*responsiveness*) 5. Ability to develop and grow (*growth*) 6. Ability to adapt to environmental changes (*adaptability*) 7. Ability to reproduce/pass on genetic information (*reproduction*)

Trichomes

1. Are projections from the leaf. 2. Trichomes serve a wide variety of functions, including increasing surface area (especially in roots), conferring pubescence, secreting toxins and other substances

Domain Bacteria

1. Arguably the most successful life form on the planet. 2. They diverged from their common ancestor so long ago that their true evolutionary relationships may never be fully known. 3. But they are vital components of every ecosystem on earth: -Ubiquitous -Diverse -Economically important -Ecologically vital (fixing nitrogen and decomposing) 4. Single, circular chromosome, are haploid and have an average of 1,000 genes 5. Bacteria may be: -Unicellular (individual, independent cells) (*primitive*) -Aggregate (associated/adhered cells) -Colonial (some division of labor) (*derived*) 6. *Lawn*- A bacterial colony that has grown to form a field or mat 7. Bacteria (1-5 μm) are smaller than most eukaryotic cells (100-1000 μm). 8. Double-stranded DNA is organized as the *nucleoid*. 9. Cytoplasm is enclosed (from inner to outer layer): -Fluid *plasma membrane* -Tough *cell wall* -Protective *gel capsule* (some species) 10. Bacteria may be categorized (not necessarily classified) by shape: -Spherical -Rod-shaped -Helical (spiral) -Variants of the above *Bacterial shapes do not necessarily reflect phylogenetic relationships* 11. Can have *fimbriae* or a specialized fimbria called a *pilus* used for *conjugation* 12. Can have *plasmids* which are transferred in conjugation via pilus 13. Most are *motile* and can move -*Gliding* (slime trail) -*Swimming* (flagella) -Can be *positive or negative taxis* 14. Cell wall contains *peptidoglycan* that have *NAG* and *NAM* 15. Can be *gram positive* or *gram negative* (pathogens are often gram - due to gel capsule) 16. Can reproduce sexually or asexually via *binary fission, conjugation, transformation, transduction.* 17. In phylum Firmicutes, an *endospore* may form 18. Can be *obligate anaerobes, obligate aerobes, or facultative anaerobe.* 19. Most bacteria *heterotrophic decomposers,* but they can also be *autotrophic* as photosynthetic and chemosynthetic producers. 20. Can perform *nitrogen fixation* or *denitrification* 21. Can be *pathogenic* and are often *opportunistic pathogens* 22. Can produce *exotoxins* or *endotoxins* and cause disease 23. In order for a bacteria to be classified as a disease, *Koch's Postulates* must be met

How Do Bacteria Cause Disease?

1. Bacteria can cause disease via: -*Invading and feeding on tissues.* 2. Producing *exotoxins*: -Manufactured intracellularly -Secreted into bacteria's medium >Escherichia coli >Vibrio cholerae >Clostridium spp. 3. Producing *endotoxins*: -Included in the cell's plasma membrane -Produced primarily by G- bacteria -Affect the host when the plasma membrane is lysed >Salmonella spp. 4. An *iatrogenic* infection is one that is caused by the healer or the place of healing.

Bacteria reproduction

1. Bacteria can reproduce either asexually or "sexually" (i.e., with genetic recombination) -*Binary fission* (asexual cloning) -*Conjugation* (genetic recombination)- donor to recipient bacteria -*Transformation* (genetic recombination)- take from environment (non-identical daughter cells) -*Transduction* (genetic recombination)-viral intermediate (identical daughter cells) 1. *Sexual reproduction* is defined as the production of new living organisms via combination of genetic information from two individuals of different mating types.

John Needham (1713 - 1781)

1. By 1745, it was well known that boiling killed microorganisms. To test whether they would reappear spontaneously after boiling, Needham boiled broth, then covered it. A few days later, microorganisms grew in his flasks. 2. Some believed this was evidence of a "life force" residing in the broth that allowed spontaneous generation. 3. But Needham's methods were imperfect: -He didn't boil long enough to kill bacterial resting stages (endospores) -He allowed the broth to cool, uncovered, to room temperature before covering it allowing plenty of time for bacterial colonization. 4. *Tried to prove spontaneous generation, and he did....but only because his methods were flawed. He left the broth uncovered and didn't boil long enough.*

Collenchyma (Simple Ground Tissue)

1. Collenchyma cells provide *pliable/flexible strength* to plant tissues. 2. Collenchyma cells: -Are usually found just under the epidermis -Tend to be elongated, rather than round. -*Have a thicker primary wall* than parenchyma cells. -Have particularly *thickened corners( -Are long-lived, like parenchyma. Examples: Flexible outer layer of broccoli stem, celery strings outer walls of growing roots, and shoots

Ciliophora (ciliates) (Alveolata)

1. Commonly known as *ciliates*, these are the most anatomically complex protists. -Covered in shortened flagella called *cilia* -One small, diploid *micronucleus* for *reproduction only*; its genes are not expressed -One large, polyploid *macronucleus* for *regulation of cell functions.* (produced by micronucleus) 2. Produced by the micronucleus, it is not passed on to daughter cells. 3. *This are the most diverse protist group, with over 8000 species.*

Joan Oro Experiment

1. Created an apparatus similar to the Miller-Urey Apparatus which yielded: sugars, lipids, amino acids (from hydrogen cyanide + ammonia in aqueous solution), adenine (from HCN) 2. Other experiments demonstrated that *dripping amino acid solutions onto hot clay or sand--as might have been found on primordial earth--caused amino acids to polymerize* into (highly cross-linked) oligopeptides.

Two Domains of Prokayotes

1. Domain Archaea (archaeans) 2. Domain Bacteria (bacteria)

What are some of the theories about synthesis of organic compounds on Early Earth?

1. Earth's early atmosphere was a reducing (electron-adding) environment, in which organic compounds could have formed from simpler molecules. The energy for this synthesis could have come from lightning and UV radiation. 2. The early oceans were a solution of organic molecules, a "primitive soup" from which life arose. 3. Organic molecules arose from "neutral" atmospheres 4. First organic compounds formed near volcanoes which have openings that may have been reducing. 5. Formed from *hydrothermal vents* which are very hot (300 to 400 degrees celsius) and have minerals coming from Earth's interiors. However, the compounds would be unstable. 6. Formed from *alkaline* vents which release water that has a high pH (9-11) and is warm (40 to 90 degrees C). 7. Arrived with meteorites that contained amino acids and other organic compounds such as lipids and simple sugars.

Waxy Cuticle (Embryophyte Synapomorphy)

1. Epidermal cells produce an *acellular layer of wax* that covers all plant surfaces. 2, Its function is to *prevent desiccation.* 3. The primitive condition, exhibited by non-vascular plants: thin cuticle that affords little protection, keeping them amphibious. 4. More derived plants have a thicker cuticle.

Epidermis (Dermal Tissue)

1. Epidermis is usually only once cell layer thick. *Leaves have both upper and lower layers of epidermis.* 2. A few plants have thicker epidermis in specific locations 3. Orchidaceae *velamen* acts as a sponge to absorb water and minerals 4. Piperaceae (Pepper Family) and some Ficus (fig) species have a thick leaf epidermis that protects against desiccation. These are usually subtropical dry forest species.

Cuticle

1. Epidermis secrete an aceulluar, waxy cuticle composed of *cutin* that helps *prevent desiccation*. 2. Vascular plants have much thicker cuticle than non-vascular plants (amphibians/bryophytes) 3. It is generally much thicker on the upper leaf epidermis than on the lower leaf epidermis.

Four Major Phases that led to the Origin of Life

1. Generation of *small organic molecules from abiotic (non-living) precursors.* (*abiogenesis*) 2. Joining of these smaller subunits into *biological macromolecules*: *Proteins*- polymers of amino acids *Nucleic acids*- polymers of nucleotides *Carbohydrates*- polymers of sugars *Fats*- polymers of fatty acids 3. Packaging of these macromolecules into *protocells*: -A membrane surrounding an internal space -Internal space containing fluid different from its surrounding medium 4. Origin of *self-replicating molecules that made inheritance possible.*

Examples of peripatric species

1. Hippos and whales 2. Grizzly and polar bears 3. California channel islands 4. Vernal sweet grass They naturally diverged and different demes didn't interact with each other until they separated

Stomates (Embryophyte Synapomorphy)

1. If you're covered in wax, you need some breathing holes. 2. Stomates are *gas exchange pores* in the leaf surface. 3. Because plants perform both photosynthesis and respiration, both O2 and CO2 come and go through the stomates. 4. Two curved *guard cells* flank the opening. 5. In higher plants, these open and close the stomate via internal turgor pressure changes.

Periderm

1. In woody plants, the epidermis is eventually replaced by *periderm*. 2. This is the woody/corky layer commonly referred to as "bark". But the bark is only one of several periderm layers. -*Phellem* (cork) is the outer layer. Its cells are dead and hollow at maturity. -*Phellogen* (cork cambium) is the lateral meristem that generates periderm. -*Phelloderm*. located just internal to the cork cambium, is composed of living parenchyma.

Animal Reproduction Cycle

1. Inside adult animal ovaries or testes, *diploid (2n) germline cells* produce *haploid (n) gametes* (ova or sperm) via *meiosis*. 2. Male and female gametes join to form a *diploid zygote*. 3. Zygote grows into a new *diploid individual* via *mitosis.* 4. The new diploid individual produces *haploid gametes* via meiosis. ...and the cycle continues.

Conjugation

1. Is the transfer of DNA from a *donor* bacterium to a *recipient* bacterium. 2. This is accomplished by means of connection donor to recipient via a *pilus*. 3. Any foreign DNA taken up by a bacterium can be incorporated into the recipient chromosome by means of a double crossover. 3. When the recipient bacterium reproduces, the two daughter cells are a product of recombination of genetic information from two individuals of different mating types.

New Sporophyte (2n)

1. Like its grandparent, the *new sporophyte* is *diploid.* -The *bryophyte sporophyte* is *annual*. -An annual plant lives, reproduces and dies in *one year/season.* -The *tracheophyte sporophyte* is *perennial*. -A perennial plant lives (and usually reproduces) for *more than one year/season.* ~The growing tracheophyte sporophyte crushes its gametophyte mom out of existence. ~Life (almost always just one season) is short and cruel for the tracheophyte gametophyte. 2. The new sporophyte will mature, produce sporophylls and spores, and the cycle will continue.

Methanogens

1. Methanogens are *anaerobic*, thriving in *oxygen-free environments.* 2. Methanogens *produce methane* as a metabolic by-product of CO2 reduction. 3. They are commonly found in the intestinal tracts of many vertebrates. 4. They are important *symbionts* in the intestines of most animals, including ruminants and humans.

What would be the advantage of plants colonizing land, as opposed to remaining in an aquatic environment?

1. More carbon dioxide in the atmosphere than in water 2. More oxygen in the atmosphere than in water 3.Fewer predators/herbivores on land than in water 4. Fewer pathogens on land than in water 5. More light on land than in water 6. Nutrients are more concentrated in terrestrial substrates than aquatic substrates

Bacteria Movement

1. Most bacteria are *motile*, meaning they can move. Mode of locomotion be used in bacterial identification. 2. *Gliding*- bacteria slide on a secreted slime trail *Swimming bacteria*- rotate one or more flagella 4. Note the differences between the prokaryotic and eukaryotic flagella: -Different protein composition (*flagellin* vs. tubulin) -Different mechanism of action (*rotating* vs. waving) -Different ultrastructure (9 + 2 array vs. *hook connected to basal body*) -*Not covered in plasma membrane, like in eukaryotes* 5. Taxis means "movement". -Bacteria exhibit *positive* (move towards) or *negative* (move away) taxis in response to environmental stimuli. *Responses to various stimuli differ among species.*

True Tissues (Embryophyte Synapomorphy)

1. Most green algae consist of relatively similar cells, each of which performs its own functions. 2. A *tissue* is an aggregation of cells coordinated to perform a particular function or set of functions. 3. *Simple tissue* is composed of *one type of cell.* Ex. Parenchyma, Collenchyma, Sclerenchyma 4. *Complex tissue* is composed of *more than one type of cell.* ex. Epidermis, Phloem, Xylem

Root Symbiosis: The Nitrogen Cycle

1. Nitrogen is a critical component of nucleic acids (DNA and RNA) proteins 2. But most organisms cannot sequester gaseous nitrogen. 3. Only a few genera of bacteria are able to perform nitrogen fixation, the conversion of gaseous nitrogen into forms that plants can use. 4. *Plants incorporate these inorganic compounds into biological macromolecules that feed all other life forms on the planet.* 5. Without nitrogen fixation, life on earth as we know it would not exist. 6. *The root cap provides a growth medium for beneficial nitrogen-fixing bacteria in the form of root nodules*

Euglenozoans (Excavates)

1. Not a plant or animal. Euglenoids are *mixotrophs*, meaning they can switch between *photoautotrophy* or *heterotrophy*, as necessary. 2. They are NOT closely related to either plants or animals. 3. Euglena is a ubiquitous mixotroph that some of us remember from after Hurricane Andrew. When the power went off and filtration stopped, these guys turned local swimming pools a lovely emerald green.

Oparin's Experiment

1. Oparin combined -Gelatin (a protein) -Gum arabic (a polysaccharide/carbohydrate) 2...and mixed them with a wavelike motion, mimicking that of the early ocean. 3. *Stable, globular coacervates formed.* 4. When lipids were added to the mixture, coacervates -Formed an even more stable membrane-like sheet. -Readily took up enzymes and substrates added to the aqueous medium. -These began to function normally inside the coacervates (*protoplast*)

Carotenoids and Animal Vision

1. Orange, red, and yellow fruits and vegetables are rich in *carotenoid pigments*, notably *β-carotene.* -Carotenoids serve as light-capturing pigments in photosynthesis. -Animals cannot manufacture *Vitamin A (retinol)* de novo -However, they can break down β-carotene to yield retinol's precursor. -Retinol serves as the light-capture component in *rhodopsins*, the visual pigments in animal photoreceptors. 3. Evolution as opportunism: *Animals could not have evolved visual systems (as we know them today) without eating the light-capturing molecules made by plants.*

Vascular tissue (True Tissue Embryophyte Synapomorphy)

1. Performs water and nutrient transport 2. *Xylem*: -Transports water and inorganic solutes -Flow direction: roots to stems to leaves in *one direction* -Transport cells dead and hollow at maturity 3. *Phloem*: -Transports aqueous products of photosynthesis, organic solutes -Flow direction: *multidirectional*, can change direction -Transport cells alive at maturity

Phylum Firmicutes

1. Phylum Firmicutes (Latin: firmus, strong, and cutis, skin) are mostly gram-positive bacteria. Their name comes from their tough, environment-resistant resting structure, the *endospore.* 2. The endospore: -Is bacterial DNA surrounded by a thick wall. -Can survive extremes of temperature and drought. -Is extremely difficult to kill. -Are formed by some important pathogenic bacteria ~Clostridium tetani ~Staphylococcus spp.

Cell Call Composition of Plant Cell

1. Plant cell walls are primarily made of *cellulose.* 2. Cellulose fibers are bundled into *microfibrils.* Microfibrils are bundled into *macrofibrils.* 3. These form a network throughout the cell wall. 4. Cell walls also contain: *Hemicellulose* -A branched *heteropolymer* of various sugars -Amorphous, conferring *little structural strength *water soluble at high pH (don't bleach your kitchen sponge!) -Not digestible by animals, but by some microbes 5. *Pectin* -A *heteropolymer* of various sugars gelatinous, sticky (we use it to thicken preserves) -Not digestible by animals, but by some microbes sometimes marketed as a remedy for high LDL ("bad" cholesterol) -However, it can interfere with absorption of ~β carotene ~Digoxin (heart medication) ~Lovastatin (cholesterol-lowering drug) ~Tetracycline antibiotics

Plastids (Viridiplantae Synapomorphy)

1. Plant cells employ a variety of organelles collectively called *plastids* 2. An undifferentiated *proplastid *can develop into a(n)... *Etioplast*- Chloroplast not yet exposed to light ~*Chloroplast* - Site of photosynthesis ~*Chromoplast* - Pigment synthesis and storage *Leucoplast*- Fatty acid and amino acid synthesis ~*Amyloplast*- Starch synthesis and storage -*Statolith*- Allows plant to detect gravity ~*Elaioplast* - Lipid storage (usually as oil) ~*Proteinoplast*- Protein storage and modification

Plant starch (Viridiplantae Synapomorphy)

1. Plants store their energy as a unique form of *starch*. -Starch is a polymer of the simple sugar *glucose.* -It is stored as tiny granules inside *amyloplasts* in the cell. -A granule consists of alternating (1) semi-crystalline and (2) squishy layers of... ~branching *amylopectin* (~75-80%) ~linear *amylose* (~ 20-25%) 2. Its (*α glycosidic*) bonds are readily broken by animal digestive enzymes. 3. These vital molecules are at the base of every ecological food web. Starch has myriad uses, in both modified and unmodified forms. It is the most important carbohydrate in the animal diet.

Photopigments (Viridiplantae Synapomorphy)

1. Plants' emerald green color is conferred by *photosynthetic pigments*: -Chlorophyll a (found in all photosynthetic organisms, including protists) -*Chlorophyll b* (Vridiplantae syn -various carotenoids (yellow, orange, red) 2. The role of these pigments is to capture *photons*, wave/particles of light energy. 3. The pigments transfer this electrical energy to biological machinery that converts that energy into the chemical bonds of carbohydrates.

Fertilization of Gametophytes

1. Rain provides the moisture sperm need to swim. 2. *Male gametophytes release their sperm*, which follow the chemical trails exuded by the *female gametophytes.* 3. Sperm swim up the female's legs and into her archegonium. 4. One sperm *fertilizes* the waiting ovum. 5. A *diploid zygote* is formed inside the archegonium. 6. The diploid zygote will continue to grow via mitosis inside the archegonium until it matures into a genetically unique, diploid sporophyte. However it will crush the megagametophyte in the process.

Plasmids

1. Small, circular pieces of *autonomously replicating DNA* 2. Usually contain only a few genes 3. *Are not considered part of bacterium's genome* 4. But may confer phenotypic traits such as: -Antibiotic resistance -Ability to produce toxins (e.g., Salmonella, Clostridium) 5. Might have come from a *pilus transfer* via *conjugation* or *transformation* from the environment

Dinoflagellates (Alveolata)

1. Some species are responsible for seasonal *red tides* that can cause massive die-offs of fish and other marine animals. 2. They are responsible for the most common form of non-bacterial seafood poisoning in the U.S., *ciguatera.* 3. Not all dinoflagellates are dangerous. 4. Symbiodinium spp. form one of the most vital symbiotic relationships on earth: *zooxanthellae and coral*

Factors that drive extinction

1. Species interactions 2. Local ecosystem changes (habitat loss) 3. Natural disasters 4. Climate Change -Glaciation -Changes in sea level

Depending on their chemical properties, organic molecules in aqueous solutions can:

1. Spread out into sheets 2. Form small clusters 3. Disperse very uniformly in the water, forming a *colloid* 4. Form microscopic, spherical droplets called *coacervates*

Three Types of Plant Organs

1. Stem (First Plant Organ) 2. Root 3. Leaf *Flowers are the best way to differentiate plants and are nothing more than fancy leaves*

Antiobiotics

1. Substances that *inhibit the growth of prokaryotic cells* (bacteria and archaeans). They are naturally manufactured by plants, fungi, and bacteria. 2. Humans use and modify naturally produced antibiotics as protection against bacteria. -A *bacteriostatic* antibiotic inhibits bacterial growth. -A *bacteriocidal* antibiotic kills bacteria outright.

Plant Sex Cycle

1. The *diploid (2n) sporophyte* plant produces *diploid germline cells*. 1a. The 2n germline cells undergo *meiosis* to produce *haploid (n) spores.* in the *sporangium* which is on a *sporophyll.* 1b. The sporangium eventually breaks open and releases mature spores. If a spore is lucky enough, it will find a moist, hospitable spot and *germinate.* 1c. Each spore grows via mitosis into a *haploid (n) gametophyte* 1d. The gametophyte produces *haploid (n) gametes* via *mitosis* in the *gametagium* 2. During a rain storm, the *anteridium* releases *sperm* which swims to the female *archegonium* which contains the *ovum.* *Fertilization* takes place inside the archegonium. 3. The *zygote grows via mitosis* into a new *diploid sporophyte*. This continues to happen in the archegonium until it bursts open as a *new sporophyte* (this happens to tracheophytes). 4. The *sporophyte* produces haploid *spores* via *meiosis.* 5. The cycle repeats

Complex Tissue: The Dermal System

1. The *epidermis* and *periderm* serve as a plant's outer covering. -*Epidermis* covers young stems, young leaves, and mature leaves. -*Periderm* covers roots and stems *after secondary growth* (widening from the secondary meristems or *cambia*). 2. *Herbaceous plants* retain epidermis all their lives. 3. *Woody plants* start their lives as herbaceous plants. When young, they have epidermis. 4. As a woody plant matures, however, the epidermis sloughs off and is replaced by *periderm*. *Periderm is found only in woody plants.*

Three Systems of Tissue

1. The *ground system* (parenchyma, collenchyma, sclerenchyma) forms the soft tissue "bulk" of the plant. 2. The *dermal system* forms the external "skin" of the plant (epidermis and periderm) 3. The *vascular system* (xylem and phloem) provides water and nutrient transport.

Root cap

1. The *root cap (= calyptra)* is a sheath of parenchyma cells surrounding the growing root tip. 2. The root cap: -Is produced by the apical meristem -*Protects* the delicate tip and apical meristem from abrasion -Tells the root tip which way is down (roots are *gravitotropic*) ~Specialized root cap cells (*statocytes*) act as *gravity sensors.* ~Statocytes contain amyloplasts (w/ starch granules). ~Inside the cell, the granules fall towards gravity. -Root tip grows in the direction of the amyloplasts. -Remove the root cap, and the root tip will grow in random directions. 3. Outer root cap cells produce slippery *mucilage* that: -*Lubricates* the root as it grows through the soil -Provides a growth medium for *beneficial nitrogen-fixing bacteria* 4. Still, the root cap cells are constantly abraded off and replaced from within.

Zygote (2n)

1. The *zygote* is diploid. 2. Inside the gametophyte's *archegonium*, the zygote will grow via mitosis. 3. Eventually, it will emerge from the archegonium as the *new sporophyte (2n).*

Young *Woody* Stem (cs)

1. The architecture of a young woody stem is similar to that of an herbaceous stem, but it will have an extra layer of periderm bark. *Epidermis* - will eventually be replaced by bark *Cortex* - will eventually be replaced by bark *Phloem* - transports organic solutes in water *Vascular cambium* (secondary meristem) - gives rise to secondary xylem & phloem *Xylem* - transports inorganic solutes and minerals in water *Pith*- will eventually be replaced by xylem *But in a wood species, the *vascular cambium* (secondary meristem) will give rise to: *Secondary xylem* (wood rings) *Secondary phloem* (the innermost layer of bark) Vascular and cork cambium are absent are absent in an herbaceous plant.

Bacterial Cell Wall

1. The bacterial cell wall contains *peptidoglycan*, lattice of *amino acids* cross-linking two sugars: -N-acetyl glucosamine (NAG) -N-acetyl muramic acid (NAM) (unique to bacterial cell walls) 2. Peptidoglycan forms a thick, rigid layer in the cell wall. 3. The layer varies in location and thickness among species. 4. Cell wall composition can serve as a diagnostic character in bacterial identification. (Exception: *mycoplasmas*, intracellular parasites, lack a cell wall.)

Cell wall (Viridiplantae Synapomorphy)

1. The cell wall surrounds the plasma membrane. It provides: -*Tensile strength* (resistance to breaking under tension) -Protection against mechanical stress -Some degree of filtration 2. *The cell wall helps the cell maintain its shape despite osmotic changes.* -A normal supply of water keeps the central vacuole full. -*Turgor pressure* is the force of the cell's liquid contents against the cell wall. -Under drought conditions, the vacuole shrinks, the cell becomes *flaccid* and extreme/prolonged hypertonic conditions will result in *plasmolysis* -The cell wall helps retain infrastructure until water is restored and the cells become *turgid* again.

Which were probably the first land plants?

1. The first land plants were *green algae*, affectionately known as "pond scum". They appeared on wet shores during the Cambrian, 500-600 million years ago. 2. These ancestral algae had few, if any, specialized cells lacked true tissues gave rise to small, amphibious descendants that had primordial tissues and lacked vascular tissue. 3. The descendants of these *amphibious plants* are the *non-vascular* plants: -Liverworts -Hornworts -Mosses

Gametophyte (n)

1. The gametophyte is a *haploid (n), gamete-producing plant.* 2. Gametogenesis takes place in a *multicellular sex organ (n)* called a *gametangium* (generic term), which is either: -An *archegonium* (female) -An *antheridium* (male) 3. They are the dominant cycle for bryophyte while the ephermal for tracheophytes. 4. Doesn't have organs, has a *thallus*

Seed Plant Gametophytes: Female

1. The gametophytes of female seed plants are even more reduced. 2. The seed plant female gametophyte remains encased in sporophyte tissue throughout its life. 3. Sporophyte integuments + gametophyte comprise the *ovule*. 4. After fertilization, the ovule becomes a *seed.* 5. The sporophyte integuments form the *seed coat.*

The Leaf

1. The leaf is the plant kingdom's most evolutionarily recent organ. It is the *primary site of photosynthesis and gas exchange.* 2. The leaf has undergone more evolutionary diversification and specialization than either stem or root. 3. There's a modified leaf for just about everything: -Protection from herbivores -Reducing water loss -Storing water -Storing food -Holding toxins -Climbing other plants -Attracting pollinators for sex -Trapping and digesting live animals

Sporophyte (2n)

1. The sporophyte is a *diploid (2n) spore-producing plant*. 2. When reproducing, the sporophyte produces specialized leaves called *sporophylls* that bears *sporangia.* 3. In *tracheophytes,* sporophytes are the dominant cycle, while in *bryophytes* they are the ephermal/seasonal stage.

Multicellular Sex Organs (Embryophyte Synapomorphy)

1. Unlike green algae, land plants have multicellular sex organs. These appear only in the *gametophyte.* 2. The sex organs are generically known as *gametangia* (Greek: angion, "box"). 3. *The female gametangium* -Is known as the *archegonium* -Produces *ova* via mitosis -Is somewhat analogous to the animal *ovary* 4. The male *gametangium* is: -Known as the *antheridium* -Produces *sperm* via mitosis -Is somewhat analogous to the animal *testis* 5. *Sperm* are released (from the *antheridium)* when the environment is wet. They swim to the *ovum*, still nestled in the *archegonium*. Fertilization takes place inside the archegonium. This produces a *diploid zygote.* The zygote is protected and continues to develop into a sporophyte until the archegonium bursts.

Xylem Cells

1. Xylem conducts water and minerals through: *Tracheids* (more *primitive*) -Dead & hollow at maturity -Tapered at each end -Perforated with many pores -Relatively narrow diameter lumen -Lie end-to-end with tapered ends meeting -Form long conducting tubes *Vessel elements* (more *derived*) -Dead & hollow at maturity -Open at each end -Perforated with many *pits* -Relatively wide diameter lumen -Lie end-to-end to form *xylem tubes* -*Perforation plate* separates pairs of vessel elements 2. Xylem *metabolism* and *structural support* is provided by: parenchyma (form live *rays* that conduct water laterally), collenchyma, sclerenchyma 3. Xylem is *highly lignified.*

SAR Clade

A diverse probably not monophyletic clade of protists: 1.*S*tramenopiles: fuzzy flagellum paired with a smooth one (all photoautotrophs) -*Bacillarophyta* (Diatoms) with silica shell -*Chrysophyceae* (Golden Algae) with chlorophyll c -*Phaeophycae* (Brown Algae) with fucoxanthin 2.*A*lveolates: Have sac-like *alveoli* under the plasma membrane and these small vesicles form a *pellicle* that maintains the cell's shapes -*Dinoflagellates* are responsible for red tides and have a symbiotic relationship (zooxanthellae) and coral -*Apicomplexa* are parasitic "sporozoans" with a apicoplast and are host specific -*Ciliophora (ciliates)* are covered in cilia and have a micronucleus for reproduction and a macronucleus for regulation. They are the most diverse protist group. 3.*R*hizarians: related shelled and unshelled *amoebas* that have *pseudopods* -*Foraminifera* have calcium carbonate shells and the pseudopods emerges from holes in the shell -*Radiolaria* have shells of silica and also have holes in their shells for their pseudopods

Flower

A flower is a whorl of leaves called *sporophylls* that are specialized for reproduction,

Ring species (Parapatric speciation)

A geographically contiguous series of neighboring demes, each of which can interbreed with neighboring demes, but for which there exist at least two "terminal" populations too distantly related to interbreed. *There's gradation*

Incipient species

A group of organisms that is about to become a separate species from other, related individuals

Primary endosymbiosis

A larger cell engulfs a smaller cell, which then takes up residence to the benefit of both cells.

External Anatomy of a *Leaf* (Not Cross Section)

A leaf consists of *blade and petiole.* The wedge-shaped space between the stem and petiole is the *leaf axil.* An *axillary bud* is located on the stem at each petiole's base. It contains an apical meristem, the source of *side branches.* Some leaves lack a petiole, and are attached directly to the stem. These are said to be *sessile.*

Basal taxon

A lineage that diverges early in the history of a group and remains relatively unchanged

Colloid

A mixture containing small, undissolved particles that do not settle out.

Protocooperation

A mutually beneficial interaction between organisms in which the interaction is not physiologically necessary to the survival of either (+, +)

Bryophyte

A primitive *nonvascular* plant where *gametophyte* (n) is the *dominant* life cycle stage, whereas the *sporophyte* (2n) is small and *ephemeral/seasonal.*

Pseudobulb

A pseudobulb is a modified stem unique to orchids. They are *thickened, bulblike stems that store both water and nutrients.*

Commensalism

A relationship between two organisms in which one organism benefits and the other is unaffected. (+, 0)

Parasitism

A relationship between two organisms of different species where one benefits and the other is harmed (+,-)

Amensalism

A relationship in which one organism is harmed and the other is unaffected. A prime example of amensalism is penicillin killing bacteria. The bread mould penicillium secretes penicillin that ultimately kills bacteria. *No one benefits like in parasitism* (-, 0)

Rhizomes

A rhizome is an *underground stem*. It can be distinguished from a root by the *presence of nodes*, from which new aerial stems may emerge. Ferns and many other plants propagate asexually via rhizomes.

Endospore

A small, rounded, thick-walled, resting cell that forms inside a bacterial cell. They are very tough, have an environment-resistant resting structure.

*End*emic species

A species native to a particular area and found nowhere else on earth.

Exotic species

A species that has been *introduced anthropogenically* to an area where it did not evolve. Many ornamental plants fall into this category. As long as they do not escape cultivation and invade native ecosystems, they are not problematic.

Indicator species (bioindicator)

A species that, by its presence, abundance, lack of abundance, or chemical composition, * demonstrates* some distinctive aspect of the *character or quality of an environment.*

Keystone species

A species upon which many other species in an ecosystem rely for survival; a species that is more critical. Ex. Krill, marine plankton species, coyote in chaparral, honey bees, wolves, sea otters

Native/indigenous species

A species whose presence in a particular region is the result only of natural processes, with no human intervention.

Stem Layers in Cross section (cs)

A stem is basically a cylinder made up of concentric layers of tissues. From external to internal layer, a generalized stem consists of 1. *Epidermis* - complex tissue is a protective barrier 2.*Cortex* - composed mostly of parenchyma 3. *Phloem* - transports water and organic molecules made by the plant 4. *Vascular cambium* - lateral meristem 5. *Xylem* - transports water and minerals from the soil 6.*Pith* - composed of parenchyma

Stolon

A stolon is an *above ground stem that grows horizontally*. It takes root at points along its length and sprouts new plants. Stolons are another means by which plants can propagate asexually, producing a clone.

Embryophyta Synapomorphies

A subkingdom of Viridiplantae that includes only land plants (*excludes green algae*). 1. Characterized by their synapomorphy of the plant embryo develops inside the multicellular sex organ (*archegonium*) of its female parent, therefore it has a *protected embryo*. 2. Multicellular sex organs, generically known as *gametangia* (female archegonium and male antheridium) 3. *Heterogamy* (anisogamy)- male and female gametes are physically distinguishable 4. *Meristem* tissues that are embryonic and totipotent 5. *True tissues*- lands plants have simple tissue and complex tissue 6. *Waxy cuticle* and *Stomates* to prevent desiccation 7. *Secondary metabolites* derived from primary metabolites

Foraminifera (Rhizaria)

These aquatic amoebas secrete shells of *calcium carbonate.* Highly derived, threadlike *pseudopods* emerge from holes in the shell.

Present Atmospheric Level (PAL)

By about 600 million years ago, atmospheric O2 levels were about 1% of Present Atmospheric Level (PAL). At this point: -Cellular Respiration replaced fermentation as the most common metabolic pathway (since it was the most adaptive/efficient). -An ozone (O3) layer started to form in the upper atmosphere -Ozone shielded microorganisms from lethal ultraviolet (UV) and gamma radiation. -Oceanic shallows and wet terrestrial areas could now be colonized. -By about 400 million years ago, the earliest plants were established on land. -Atmospheric oxygen levels were about 10% PAL, and continuing to creep upwards. -Today's atmosphere is about 21% oxygen, thanks to photosynthesis.

Three Primary Meristems

Called *Zone of Elongation* where region is elongating and beginning to differentiate. 1. *Protoderm*will give rise to epidermis (multipotent) 2.*Procambium* will give rise to vascular tissues (multipotent) 3. *Ground meristem* will give rise to ground tissues (multipotent)

Interfascicular cambium

Cambium that develops *between* the vascular bundles.

Fascicular cambium

Cambium that develops *within* the vascular bundles, producing secondary xylem and phloem

Character displacement

Changes in the competing species' morphology associated with resource partitioning are often accompanied by this 1. Accentuation of differences among species when they are sympatric (species tend to be more different if their habitats overlap; sympatric) 2. Minimization (or loss) of differences among species when they are not sympatric (habitats don't overlap; allopatric)

Contractile Roots

Contractile roots are most often found at the base of a corm, bulb, or other underground structure. During drought, they *expand and contract vertically, pulling the bulb deeper into the soil* to a level appropriate for its species and the environmental conditions.

Why would protocells have evolved to store their genetic information in DNA rather than RNA?

DNA is a more chemically stable repository and can be replicated more accurately.

The Convention on Biological Diversity

Defines biodiversity as "the variability among living organisms from all sources including, inter alia (i.e., "among other things"), terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are a part; this includes diversity within species, between species, and of ecosystems."

International Union for Conservation of Nature (IUCN)

Devised eight levels that describe species on the basis of population status: -*Least Concern (LC)*- not in trouble, humans -*Conservation Dependent (CD)* -*Near Threatened (NT)* -*Vulnerable (VU)*-lemming -*Endangered (EN)*- sea otters -*Critically endangered (CR)* -*Extinct in the Wild (EW)*- present only in captivity -*Extinct (EX)*

Antibiotics (Mechanisms of Action)

Different antibiotics attack different aspects of the bacterial life cycle. 1. *Inhibition of enzymes involved in peptidoglycan biosynthesis* (e.g., penicillins) 2. *Interference with normal nucleic acid (DNA, RNA) function and repair* (e.g., fluoroquinolones such as ciprofloxacin, enrofloxacin) 3. *Interference with tRNA function and/or ribosome function* (e.g., macrolides, chloramphenicol) 4. *Disruption of the plasma membrane* (e.g., polymixins; imidazoles) -Some of these weakly bind eukaryotic plasma membranes. -This limits their use to topical applications (e.g., neosporin).

Pathogen

Disease-causing agent

Resource Partitioning

Dividing a common resource so that each competing species uses only a portion of that resource.

Breeds

Domesticated animals

Cultivars

Domesticated plants

Protocells

Droplets with membranes that maintained an internal chemistry different from that of their surroundings; *Oparin* considered a coacervate containing working enzyme systems to be a protocell/protobiont.

Mitosis

Eukaryotic cells can reproduce asexually via *mitosis.* Prokaryotic cells undergo the less complex asexual process of fission. *Lacking linear chromosomes, prokaryotes do not undergo mitosis or meiosis.*

Derived Ribosomes

Eukaryotic cells have characteristic 80S ribosomes, each consisting of four molecules of RNA complexed with many proteins.

Psuedopods

Extensions of cytoplasm for movement and feeding; "fake feet"

The process of binary fission and mitosis involves duplication and distribution of linear chromosomes. (True/False)

False, binary fission involves *circular * chromosomes, not linear ones.

A protobiont (protocell) has all the properties of life. (True/False)

False, it only has some of the properties. *Only had metabolism and anatomy*, they couldn't evolve, reproduce, respond to stimuli or have genetic information.

Kingdom Protista is still a thing. (True/False)

False, new DNA data and research has revealed there's not really a Kingdom Protists and previous monophyletic relationships were deemed false.

Pollen are sperm. (True/False)

False, they are fully mature reduced gametophytes.

The modes of speciation are mutually exclusive (True/False).

False, they are not mutually exclusive and are actually intertwined. For instance, ecological speciation can lead to parapatric speciation. Ex. Hawthorne flies

Northern Spotted Owls

Feed on voles. Voles eat mycorrhizal fungi. And the owls and the voles spread the fungi through their poop. These interactions are essential for forests since the fungi shares a symbiotic relationship with trees, and make they more robust and bigger. *Less Northern Spotted Owls indicate that there might be an issue with mycorrhizal fungi.*

Vertical Gene Transfer

Flow of genetic information from parent to offspring

Food Storage Roots

Food Storage Roots *sequester starch*. The plant draws on this store for metabolic activities later in the season, such as flowering. Carrots, beets, turnips, and sweet potatoes are familiar examples.

Parapatric speciation

The evolution of a new species from an ancestral species without extrinsic geographic barriers to gene flow. -The population is continuous. -The population does not mate randomly. -*Individuals are more likely to mate with neighbors than distant individuals* -This creates a cline of genotypes. -Individuals at opposite ends of the range are reproductively isolated. -It is sometimes considered a form of *ecological speciation*. -*There's reduced gene flow, some gradations that can interbreed, but at one point, the gradations on either side of the ring can't interbreed. There's reduced gene flow based on proximity.*

Peripatric speciation

The evolution of a new species when an isolated peripheral deme/population undergoes reproductive isolation from its ancestral population due to *reduced gene flow.* The daughter species move to an environment where they can't interact with their parents anymore. (There's a lot less gene flow)

Protected Embryo (Embryophyte Synapomorphy)

The fertilized zygote is not released to the environment, as it is in most green algae. Instead, it is *retained inside the female archegonium*, where it grows and develops into the sporophyte.

Sympatric speciation

The formation of a new species as a result of a *genetic change* (ex. polyploidy; allopolyploidy) or *differential resource utilization* (ecological, different niches; resource partitioning and associated character displacement) that produces a reproductive barrier between the changed population (mutants) and the parent population. *No geographic barrier is present.*

Macroevolution

The genesis of reproductively isolated populations from an ancestral population. -New species evolve from pre-existing species -*New species remain nested in the ancestry of their predecessors.* 1. Birds give rise to birds. 2. Frogs give rise to frogs. 3. Yeast give rise to yeast 4. *Parents do not give rise to offspring drastically different from themselves.* -Speciation is a temporal process- *it happens over time* -Populations exist in various stages of speciation at any given time. -Extant populations are even now undergoing microevolutionary changes. that may eventually give rise to new species.

Kinetoplastids (Excavates)

The kinetoplastids Trypanosoma spp. can cause serious parasitic diseases. -Chaga's Disease -Leishmaniasis -African Trypanosomiasis ("sleeping sickness")

Late Devonian Extinction (365 mya)

The main casualties of this event were benthic invertebrates jawless fishes, and placoderm fishes living in shallow water ecosystems, primarily in the tropics. The causes are still controversial, with candidates including asteroid impact global anoxia plate tectonics sea level change climate change *expansion of tropical, terrestrial plants.* Massive shale deposits from this period indicate large-scale organic detritus buildup. Terrestrial plant matter may have caused eutrophication and anoxia in tropical shallow waters (*the decomposition of the plants depleted a significant amount of oxygen*). About 20% of all animal families and 70-80% of all animal species died off.

Spontaneous generation

The mistaken hypothesis believed by ancient Romans stating that *life could arise from nonliving matter.*

Stramenopila (SAR Clade)

The name comes from their *fuzzy flagellum* (stramen ("straw") and pilos ("hair"), Latin). The fuzzy flagellum is often paired with a smooth one. *All* stramenopiles *have flagella*, even if only during the reproductive cycle. Includes (all photoautotrophs): 1. *Bacillarophyta* (Diatoms) with *silica shell*- produces chlorophyll and c 2. *Chrysophyceae* (Golden Algae)- produces *chlorophyll* a and *c* 3. *Phaeophycae* (Brown Algae)- produces chlorophyll a, c, and *fucoxanthin* (brownish carotenoid)

Acritachs

The oldest known eukaryote fossils (2.1 billion years old, from pre-Cambrian fossil beds in Michigan) are the *acritarchs*, from the Greek acrit = "confused" arch = "beginning

Abiogenesis

The origin of life from inorganic precursors; *spontaneous generation of organic molecules*

Pericycle

The pericycle is a cylinder of *meristematic cells* lying just internal to the endodermis. It is a lateral meristem responsible for *generating lateral (branch) roots part of the root vascular cambium.*

Genome Arrangement (of Eukaryote)

The primary genome of a *prokaryote*: -Is contained on a *single, circular chromosome* -Consists of "naked" DNA unassociated with proteins The primary genome of a *eukaryote* is contained on: -Multiple, linear chromosomes -Consists of DNA molecules wound around histone protein complexes

Ecological speciation

The process by which natural selection operates on organisms interacting with their environment and each other, resulting in reproductive barriers between populations

Root

The root is the first organ to emerge from a seed. Its functions are: 1. Anchor the plant to its substrate 2. Absorb water and inorganic substances from the substrate 3. Conduct the above upwards to the rest of the plant 4. Production (in meristems) of certain hormones 5. Production of secondary metabolites 6. Storage of nutrients as carbohydrates and/or lipids

Competition

The struggle between organisms to survive in a habitat with limited resources

Ecological niche

The sum of a species' use of the biotic and abiotic resources in its environment 1. Its role and position in its environment 2. The ways it acquires food and shelter 3. Its survival mechanisms 4. Its reproductive strategies and natural history *Ecological interactions between species and their environment drive natural selection and speciation.*

Lateral Gene Transfer (Horizontal Gene Transfer)

The transfer of genes from one unrelated species to another, rather than from parent to offspring

Coyotes in Chapparel

Their removal causes a crash in the bird population since usually they feed on the predators of birds such as foxes and skinks.

Zea mays on the Brink of Extinction

There was a viral blight that attacked highly inbred U.S domestic corn. *Domestic corn* (2n = 20) was highly susceptible to the virus, while it's close relative (Zea perennis, 2n = 40) was resistant. Zea diploperennis (2n = 20) was found and is perennial, and also resistant to the virus, and was successfully able to hybridize with domestic corn.