Gen Bio 2 Study Guide, final

Define and explain what a phylogenetic tree is.

○ A phylogenetic tree is simplification, branch point signifies speciation

○ Family tree is a tree organizing species of organisms based up on homologous

traits and tracing back to the most recent common ancestors (placing organisms in

order of evolution

Did humans come from (evolve from) monkeys?

Humans did not evolve from monkeys, we share a common ancestor but species diverged into two separate lineages

What is a homology? A homoplasy? What are some examples?

Homologous structures are same structure, but different functions ○ A homoplasy is shared character not inherited from a common ancestor.

Analogous structures that arose independently, a similar structure or molecular sequence that evolved independently in two species.

■ Analogous structures are different structures, but same function

What is a clade?

A clade is a group of species that includes an ancestral species and all of its descendants.

MRCA?

MRCA is most recent common ancestor

Monophyletic?

all descendants and common ancestors

paraphyletic

consists of an ancestral species and some but not all its descendants

Polyphyletic

animals are placed in groups based upon homoplasies

ancestral

most primitive characteristic, not evolved

derived

evolutionary novelty unique to a clade, what a more current organism

has that the previous didnt.

what is a synapomorphy?

A unique, derived, homology (Defining feature)

What is an outgroup?

An outgroup is a closely related species or group of species from a lineage that is known to have diverged before the lineage that includes the species we are studying (the ingroup).

How is the outgroup chosen?

Closely related taxon with ancestral traits.

■ Outgroups give polarity to a phylogeny

Roughly how long ago (to the nearest 1⁄2 billion years) ...did life originate? ...did eukaryotic cells originate? ...did animals and plants originate?

○ Earth originated 4.5 billion

○ Life originated 3.5 billion years ago

○ Earliest fossils are of prokaryotes

○ Chemical and physical processes could have produced simple cells through the

stages

Miller/Urey experiment

What are the 3 metapatterns, and the corresponding features of cells, associated with the origin of life?

Genetic information, membrane, metabolism

What are the 3 hypotheses for the order in which these features emerged

Genes first, RNA world: Suggests first life was self-replicating RNA

Metabolism first: Self-sustaining networks of metabolic reactions may have been the first simple life possibly near undersea hydrothermal vents providing continual chemical precursor supply

Lipid first: Phospholipid bilayer needed to originate first in order to have everything compartmentalized inside

What are the roles of energy and protected micro spaces in the origin of life? You don't have to know the various hypotheses of where life originated.

What was LUCA? In general terms, how do the 4 hypotheses of LUCA differ?

Last universal common ancestor

Micro caves in undersea volcanic vents, metabolism first (iron-sulfur world).

What are the 3 domains of life?

Archaea, bacteria, eukarya

Who are prokaryotes?

archaea and bacteria also they are single celled.

What kind of link does Archae have?

ether link, there is no disease in archae.

what about in Eukaryotes & bacteria?

ester link, If you make a drug that kills bacteria it can possibly kill us too because of the ester link

What is the ecological importance of viruses?

○ Viruses are immensely important to the turnover of biomass in many ecosystems

○ Most of these viruses are bacteriophages, which are harmless to plants and animals. They infect and destroy the bacteria in aquatic microbial communities, comprising the most important mechanism of recycling carbon in the marine environment. The organic molecules released from the bacterial cells by the viruses stimulate fresh bacterial and algal growth.

○ TINY PREDATORS

○ Abundant, infetal organisms , huge C sink genetic vector and reservoir,

What are the key features of viral structure?

○ Genome(RNA or DNA)

○ Capsid(protein)

■ MAY HAVE

Envelope(membrane, or Envelope Proteins).

Which features necessary for bacteria to reconstruct?

Rna gene sequences

What are the key features of bacterial structure?

Cell wall, cell membrane, pilli, chromosome, cytoplasm, flagellum

■ Circular DNA

■ Nucleoid

■ Main Chromosome

■ Peptidoglycan cell wall

Two kinds of bacteria?

Gram-Negative

● Thin layer of peptidoglycan, but more complex layers

● Stains PINK

■ Gram-Positive

● Thick peptidoglycan

● Stains PURPLE

Mcconkey Plate reactions?

How do most bacteria reproduce?

Binary Fission: A type of asexual reproduction common among prokaryotes wherein a cell divides giving rise to two cells, each having the potential to grow to the size of the original cell. USES MITOSIS

Supplement. Archaea, bacteria, and protists reproduce asexually by binary fission

Bacteria do horizontal gene transfer in 3 ways

● What are the 3 mechanisms of genetic recombination in bacteria? Describe them; you

don't need to memorize the names.

Transformation: the genotype and possibly phenotype of a prokaryotic cell are

altered by the uptake of foreign DNA

○ Conjugation: dna is transferred between 2 prokaryotic cells that temporarily

joined. One cell donates, one could receives through a pilus

■ Plasmid is a piece of bacterial DNA that moves the DNA from bacteria to

bacteria (virus resistance)

○ Transduction(viruses): carry genes from one cell to another

What is plasmid? What part does it take in CONJUGATION??

Plasmid is a piece of bacterial DNA that moves the DNA from bacteria to

What is a biofilm? Is it multicellular? What are the advantages of being a part of one?

Film of bacteria that adheres to any surface (holds any group of microorganisms

that stick to each other or to a surface)

○ Biofilm is a mixed species

○ Nutrient scavenging,

○ Broader habitat range

○ It is multicellular

2 Kinds of Photosynthetic bacteria?

Anoxygenic [purple-sulfur bacteria(mangroves)]

■ Oxidizes and releases sulfur (rotten egg smell)

○ Oxygenic [cyanobacteria (in biofilm)]

■ producing the Earth's atmospheric oxygen

■ releases oxygen

Are most bacteria pathogenic? In general, how do bacterial pathogens enter host cells?

○ They enter host cells through phagocytosis

○ Most bacteria are not pathogenic

What has the new (2016) phylogeny told us about bacterial and archaeal diversity (do we know most of it?) and phylogeny (might a domain be non-monophyletic?)

○ Archaea & Bacteria are paraphyletic (duh)

○ Archaea and Eukarya are sister taxa

How are archaea similar to, and different from, bacteria?

Both have cell wall

■ Only bacteria has peptidoglycan

○ Morphology is similar but gene expression

○ cell ultrastructure

■ membrane , cell wall, flagella

Spectrum Photosynthesis?

The colors that are absorbed are the colors that are not being reflected (the color you see is the color that is not being absorbed by the plant)

What is the action spectrum of photosynthesis, and why is it different from the absorption spectrum of chlorophyll?

Action spectrum of photosynthesis is the physiological activity plotted against wavelength of light

○ (chlorophyll) Mostly Blue and red, different due to accessory pigments

OK BUDDY WTF HAPPENS IN PHOTOSYNTHESIS IN 3 SECONDS AND DONT! MF! STUTTER! OR MISS A BEAT, GO!!!!!

Light reactions solar energy to chemical energy of atp and nadph

○ Calvin Cycle (Also known as Light-independent reaction) : chemical energy of

atp and nadph to reduce CO2 to sugar

○ Carbon fixation: Rubisco

■ Attaches CO2 to organic molecule

■ 1000 reactions /sec

■ Rubisco 3 reactions/sec

■ Most abundant

What is the function of Rubisco? Why is it Earth's most abundant enzyme?

■ Carbon fixation: Rubisco

● Attaches CO2 to organic molecule

● 1000 reactions /sec

● Rubisco 3 reactions/sec

● Most abundant

Present in all plants without it also no autotrophs and heterotrophs, and the calvin cycle wouldn't happen without it.

What is photorespiration? What environmental conditions favor it over photosynthesis?

○ Rubisco binds to O2, High temperature low CO2 and high O2 ratio,

photorespiration occurs when there are low levels of CO2 and high levels of O2

○ Favored when stomata are closed in hot conditions.

In general, how do C4 and CAM pathways "patch" onto C3 photosynthesis to favor carbon fixation? How do C4 and CAM differ? Why don't all plants employ these innovations?

Too expensive for plants, c4 has a bundle sheath. C4 used ATP.

○ Cam plants keep stomata closed during the day to prevent evaporation and opens

at night to collect CO2

■ Mainly in succulents (ex: cacti)

When do plants use cellular respiration?

at night when the bad b*tches come out hoe

Which other organisms besides plants use photosynthesis?

Cyanobacteria the basic b*tch that started life. she done messed up lmfao.

Why doesn't photosynthesis violate the law of entropy?

Bc photosynthesis makes its own f*cken rules don't play.

If you count the entropy of the whole system--not just what's going oninside the plant but also what's going inside the source of light that drives photosynthesis in the plant--you see that the total entropy goes up

Protists, are they monophyletic.

Nah, they're not bc plants, fungi & animals involved in the tree. Protists are

paraphyletic.

What are the derived features of eukaryotes that we discussed in class?

○ Nucleus surrounded by a membrane

○ Compartmentalization of organelles

Describe the hypothesis of primary endosymbiosis of mitochondria and chloroplasts.

What cellular and molecular evidence supports it?

Endosymbiosis is a symbiotic relationship in which one organism lives inside another, archaeal cell engulfed a bacterium, made mitochondria and chloroplasts Inner membranes of both organelles have enzymes and transport systems that are homologous to those found in the plasma membrane of living prokaryotes Mitochondria replication similar to prokaryotes and circular dna

Similarity to prokaryotes

Transcribing dna into proteins by having ribosomes

evidence for that whole cell ate photosynthetic organism theory?

Chloroplasts membranes, algal cell engulfing vesicle, chloroplaste(2)

whats multicellularity? How is it an advantage?

Multicellularity means (consisting of more than one cell), single species, division of labor, some cells give up reproduction

Larger organisms, more complex.

What are 3 examples of harmful or pathogenic protists?

Kinetoplastids from group Trypanosome, Plasmodium, Giardia

What is an ocelloid, and why is it remarkable?

Image forming eye, jump in complexity

Define gametophyte and sporophyte. Contrast their ploidy and reproduction.

○ Haploid gametophyte Mitosis (sex)

○ Sporophyte Diploid Meiosis (virgins by force how f*cken weak)

Are embryos of plants homologous with embryos of animals?

yuh

r u gonna f*cken pass this bio final

yes, if u study more. lets f*cken rage, where the energy drinks @??????

Discuss the plant tree of life as a sequence of innovations, each building on the last. Identify a plant as a "Bryophyte", Lycophyte, Monilophyte (fern), Gymnosperm, or Angiosperm based on the innovations it has, as shown in a description or illustration.

○ bryophyte= Closest living descen(need water for sexual reproduction)

■ liverworts= umbrella and cups

■ mosses= (females- archegonia and males- antheridia)

● Tall brown stick (sporophyte) coming out of green leaves (gametophyte)

■ hornworts= little green sticks (sporophyte) coming out of green mush (gametophyte)

○ lycophyte= leaves are extensions of stems

○ Fern

■ Whisk fern= sporangia= orange balls

● small grass roots= gametophyte

■ horsetails= segmented stocks with brown honeycomb like structure at top

■ Ferns

○ Bryophytes, lycophytes, and ferns produce spores, but not seeds. They are

seedless plants.

Plant phylogeny of seed plants??

○ gymnosperms= cones

○ angiosperm= flowers

also check pic on study guide if ur an intense plant idiot.

Adaptations to the terrestrial life:

Form Waxy cuticle & stomata to protect from desiccation

■ Forming Tracheids to move water and nutrients from the soil and sugar

from the leaves to the rest of the plant, etc.

■ Shifting to a dominant diploid generation to deal with the mutation of UV

radiation.

What were the advantages to plants of evolving greater height? What two major structural innovations allowed plants to greatly increase their height?

○ Competition for sunlight, better dispersal, protection from predators

○ Apical meristem height

○ Lateral meristem width

How are some plants adapted as mangroves, epiphytes, carnivores, or parasites? Identify

from descriptions or illustrations.

Adapting to challenging environments helps because little competition

○ Carnivorous plants developed attractive features to draw mosquitos in bc it lives

in nutrient poor soils

○ Parasitic plants adapted by sniffing out its prey

What are the differences in function in xylem vs. phloem?

○ xylem= carries water and flows in only one directions (up)

○ phloem= carries nutrients and flows in two directions

How is water transported upwards in a tree, at no energy cost? Explain the roles of water potential, diffusion, adhesion, cohesion, and evaporation of water.

Water moves from high concentration of water to low concentration of water (root to top)

○ Water from soil enters root through dispersion

○ Since there is less water in the air around the leaf than in the leaf evaporation occurs

○ As it evaporates it pulls the water molecule that are behind it up

Cohesion: Water is attracted to water. Adhesion: Water is attracted to other substances.

How does a leaf regulate its water loss and gas exchange? How is this a trade-off?

○ Through stomata

○ Trade off is that they close in very dry temps but this stops transpiration (water

moving throughout a plant) and photorespiration (take in O2 and let out CO2)

occurs

How does wood form? How can it tell us the age and history of a tree? Interpret an

illustration or description of a woody stem cross-section.

The result of laying down layer after layer of xylem

○ We can tell by the thickness & other properties of the rings

■ In rainy years ring is thicc (think rainy as prosperous, lots of food)

■ In dry years ring is thin (dry, like my wallet rn and thats why I be starving, therefore thin)

■ Scars from forest fires are dark deep lines in rings

How does a having a vascular cylinder, a ring of vascular bundles, or scattered vascular bundles determine whether or not the stem can form secondary growth? Which arrangement is seen in "dicots," and which is derived in monocots?

○ Vascular bundles in a ring allows for secondary growth bc of the vascular cambium in the ring

○ dicots= ring

○ monocots= scattered

What is that question about which one u can cut a whole through?

has to do with the fact that xylem is dead and phloem is alive

Phosphate deficient?

Purpler (think PP)

Nitrogen Deficient

yellow

What are the 4 whorls of flower structure, in a eudicot? What are their functions?

Carpel (female function), petal (attract pollinators), stamen (male functions), sepal (support & protection)

ok this is slightly disturbing but here's how to remember:

-carpel sounds like carpet and yeah so yeah ;)

-petal well duh its pretty 4 pollinators

-stamen think stamina and men are said to have a lot of that so ya

- sepal (bear with me) think senpai and like in all those cringe memes people say senpai supports and protecc

Contrast relatively how long it takes for gymnosperms vs. angiosperms to have sex.

Angiosperms have sex quicker like teenage weak bois who last a whole two seconds

What are the two main morphologies of fungi? How are they different?

○ Hyphae - fine threads that are the basic structural units of fungi a long, branching filamentous structure of a fungus, oomycete, or actinobacterium. In most fungi, hyphae are the main mode of vegetative growth

○ Mycelium - collective mass of all the hyphae in a fungal organism

How do mycelial fungi grow and feed? How do they disperse?

○ Made up of more than one genetic individual (parents & offspring together)

○ Spores disperse & hyphic that grow from them are haploid. Sometimes the

hyphae which eventually do meiosis to form sexual spores

○ They feed by secreting digestive enzymes outside of the cell & digesting the food

outside the body

honestly wtf is mitosis, meiosis, haploid and diploid?

soo haploid means n

diploid has 2n they have a pair of both chromosomes

mitosis makes identical of what it started with, many asexual beings use this to replicate however bad bc if one virus kills one, it can wipe out everything. Makes all cells other than gametes. Growth, repair, and asexual reproduction.

meiosis: cell splitting. makes 4 haploid out of diploid. Makes gametes for sexual reproduction.

How is a chytrid fungus affecting amphibian biodiversity?

Motile zoospores get under the stein of the frog and harden it so they can't breathe chrazy right?

How does each partner in a mycorrhizal ("fungus-root") benefit? What is connected by

the mycorrhizal network, and what are its hypothesized benefits?

mycorrhiza= the partners benefit each other because the plants gain a larger surface area and are able to obtain more nutrients for the plant

Help transfer nutrients to plants in high pH soils

What is the rhizosphere?

The biodiversity at the roots

what are leaf endophytes, and what are their benefits to plants?

Fungus inside of leaves that help benefit that leaf by preventing ants from eating it and protect them from herbivory and disease

what is a is a lichen, and how are they useful to conservationists?

Mutualistic relationship between a fungus and cyanobacteria or green algae, useful to conservationists because they can be bioindicator of pollution in the air

much lichen= happy environment

no lichen= pollution, acidic air

What ecosystem services do fungi provide?

Mycorrhizae (mutualistic relationship between fungi and plants' root) , decomposition, food webs

What are the main features of animals

Multicellularity with patterning

■ Using Hox or Hox-like genes ○ Body symmetry

○ Embryo with blastula

○ Diploid life cycle with larva

○ Collagen in extracellular matrix

Identify lack of symmetry, radial symmetry, or bilateral symmetry in an animal.

.

○ Lack of symmetry= asymmetry in sponges

○ Radial symmetry=symmetry around central axis (ex: jellyfish or starfish)

○ Bilateral symmetry=being divisible into two symmetrical halves

What are the advantages of having larva and adult stages in an animal life cycle?

Dispersal (marine)

○ Food resources

○ Specialization

■ Feeding

■ Reproduction

What are the main feeding and defense (from predators) strategies in animals? Identify in

illustrations or descriptions.

Predation

■ Active

■ Sit and wait

○ Grazing/ herbivory

○ Sediment/ detritus feeding

○ Filter feeding

○ Parasitism

○ Symbiotrophy

○ Be BIG

○ Hide

■ Buried

■ Camouflage

■ Hard shell

○ Escape

○ Toxins

■ Venom

■ Bad taste or effect

○ Aposematism: warning coloration

What are zygote, cleavage (radial and spiral), blastula, and gastrula? Identify on diagrams.

Zygote= diploid cells resulting from the fusion of two haploid gametes

○ Radial cleavage= type of cleavage characteristic of deuterostomes, cells divide so

that each top cell is directly over one another in the bottom plane

○ Spiral cleavage= type of cleavage that is characteristic to protostomes, cells divide

at a slight angles to one another so that no cell in top plane is directly above the cells in the bottom plane

○ Blastula= stage of embryonic development near the end of cleavage (cell division) but before gastrulation. The blastula usually consist of a hollow ball of cells (blastomeres) surrounding a fluid-filled cavity (blastocoel)

○ Gastrula= embryonic stage of an animal that has cell differentiated into germ layers following the blastula stage.

In very general terms, as shown on the diagram "Trends in development," how do an incomplete gut, complete gut, mesoderm, and coelom form, in embryonic development?

Incomplete gut= forms from gastrulation forming primary two germ layers (ectoderm and endoderm)

○ Complete gut= gut tube finishes form

○ Mesoderm= forms in between ectoderm and endoderm

○ Coelom= forms inside the mesoderm

What are the advantages of a body cavity (coelom)?

Compartmentalization of organs

○ Complex musculature and movement

○ Hydrostatic skeleton

○ Internal cushioning and movement of organs

What is cephalization, and how is it related to bilateral vs. radial symmetry?

○ Cephalization is the focusing of neurons and sensory organs in anterior part of the body

○ Allows for bilateral body symmetry because allows for organisms to see where they are going better

What are the distinguishing main features of Porifera and Cnidaria? Identify from descriptions or illustrations.

Porifera: No symmetry in adult, sponges, spicules, choanocytes.

○ Cnidaria: Symmetry in adult, two true tissue layer, incomplete gut they can eat big

food, medula & polyp, jellyfish.

Why are reef-building corals ecologically important? How do they obtain most of their

food? What is coral bleaching?

Reef-building corals are used as habitats for fish, contain diverse ecosystem,

protect coastlines from damaging effects of wave actions and tropical storms

○ Because of the algae present in their mutualistic relationship

○ Coral bleaching= the loss of zooxanthellae. When the water is too warm, the coral

eject the algae living in their tissues, causing the coral to turn completely white.

What synapomorphies distinguish Bilateria

Distinguish bilateria= blastula, gastrula (2 layers), mesoderm (3 layers)

then Protostomes and Deuterostomes within Bilateria;

Protostomes= blastopore becomes mouth spiral cleavage

○ Deuterostomes= blastopore becomes anus radial cleavage

and then Spiralia and Ecdysozoa within Protostomes?

Spiralia= spiral cleavage in embryo

○ Ecdysozoa= "idiosyncratic" cleavage in embryo (arthropods and Nematoda)

What are the distinguishing main features of Platyhelminthes, Mollusks, Annelids,

Nematodes, and Arthropods? Identify from examples or pictures.

○ Platyhelminthes(flatworms): 3 tissue layer, no coelom, an incomplete gut

(branched), monoecious.

○ Mollusks: complete gut (mouth and anus), cephalization, swims (cilia).

○ Annelids:( earthworm) hydrostatic skeleton, segmentation, complete gut, some

have cephalization some don't

○ Nematodes: (roundworm) microscopic, pseudocoelom, simple movement.

○ Arthropods: ( insects) hard cuticle made of chitin, jointed appendages, segmentation head, thorax, abdomen.

How are internal parasites adapted to that way of life?

Modifications of mouthparts and digestive enzymes that allow attachment to host and host's food supply, blood or tissue

○ Reduction of unnecessary sensory and locomotive organs in adult stages because its not required since they live in protected, optimum conditions

○ Specialized reproductive strategies to have both male and female parts asexually and large quantity of eggs

○ Resist attack by immune system by being inaccessible, adapting antigens from host and changing own antigens

Interpret a parasite life cycle, such as that of the pork tapeworm. How many hosts are

there in such a life cycle, and why is that an advantage? Which tapeworm stage is more dangerous for us to ingest: the encysted larva in undercooked pork, or the egg on unwashed vegetables?

Two hosts, intermediate (pork) and definitive host (human). Advantages are increased rate of survival, and pork is dispersal and humans would be to reproduced. It's more dangerous to digest eggs because it causes cysticercosis (cysts in brain and leg).

dentify the stories, and the ecological importance or potential applications to our lives (if discussed) of: the solar powered sea slug, cone snails, the Triton's trumpet snail, cephalopod adaptations; invasive earthworms, leeches; human- or plant-parasitic nematodes, entomopathogenic nematodes, dust mites, plant-parasitic or predatory mites, ticks, medicinal millipedes, and copepods.

Triton trumpet snail= uses radula with trigger and when trigger touched radula paralyses victim

■ Medicinal aspect of paralysis toxins

Cone snails= insulin

leeches= blood siphoning (getting rid of old infected blood)

s segmentation? Why is a tapeworm not segmented?

Division into separate parts and sections

They are acoelomate (no true body cavity)

what is ecdysis (aka molting)?

Allows for the organism to shed its skin shell layering and experience a period of

growth

What are the hypotheses for the vast diversity of insects?

The "right size" hypothesis is that insects will gain specialized traits in order to meet the specific needs of their environment