BIO all learning objectives

What is the average percentage of energy transferred from one trophic level to the other and how does this affect energy pyramids and biomass pyramids?

-10% -less and less energy as you go up, so things eating at the top get less energy and have to eat more to have enough food -there's a lot more primary producers than primary consumers than secondary consumers etc because as you go up, there's not enough food/resources to support as many of those top consumers

What are the four nucleotide bases in RNA, and what are their relationships with DNA?

-A (adenine) with U (uracil), G (guanine) with C (cytosine) -with DNA, this pairing is followed, if there is a T and A it put down, if there is an A a U not T is put down

Which purines bond with which pyrimidines? What are Chargaff's rules?

-A bonds with T (U in mRNA) -C bonds with G (H bonding works best w these pairs) -Chargaff's Rules: purine with pyrimidine (to fill 2 nm base length)

Describe the carbon cycle. What is the most common carbon in the atmosphere, what are the key pathways by which it is removed/returned, and what are their magnitudes?

-Carbon cycle: producers convert atmospheric carbon dioxide (CO2) into carbohydrates, heterotrophs eat organisms/detritus to get it, limestone/marble SLOWLY exchange carbon with animals, MOST is in bicarbonate (HCO3) in ocean, soil/atmosphere (CO2 from aerobic respiration)/plant carbon is a smaller source, volcanoes release CO2 into atmosphere, marine organisms put calcium carbonate (CaCO3) and salt in their shells → part of sediment when die and sink → tectonic shifts bring it up & erosion/weathering, also soft organisms in habitats with low O2 preventing decomposition but slowly converted to gas/petroleum/coal in fossil fuels -Most common carbon in atmosphere: CO2 -Key pathways in which carbon removed from/returned to the atmosphere: producers make CO2 into carbohydrates, heterotrophs eat each other, rocks/animal carcassas erode, bicarbonate (HCO3) in ocean, soil, volcanoes -Magnitude of above pathways: Atmosphere to Ecosystem -120 (10^15): Photosynthesis -107 (10^15): Diffusion Ecosystem to Atmosphere -60 (10^15): Respiration -105 (10^15): Diffusion -105 (10^15): Decomposition Soil -5 (10^15): Burning Fossil Fuels

Define the following in a logistic model: K N rmax

-Carrying capacity: K = number of individuals a population can support indefinitely dN/dt = rmaxN(K-N)/K -N: population size -rmax: intrinsic rate of increase (unlimited food and shelter, no predators, parasites, or disease, and a comfortable abiotic environment → per capita birth rate is very high, the per capita death rate is very low, and the per capita growth rate is as high as it can be) N (population size) Increases: less resources are available, K-N is small, r is small, population growth is little Decreases: more resources are available, K-N gets closer to 1, r is close to rmax, population growth is almost exponential Same as K: K-N = 0 so achieve ZPG (zero population growth) K Increases: ~ decreasing N Decreases: ~ increasing N Same as N: ~ as above rmax Increases: population can support more, ~ decreasing N Decreases: population can support less, ~ increasing N

Define the following in an exponential model: change in population size over time B D b d r

-Change in population size = Number of births - Number of deaths ΔN/Δt = B - D = (b - d)N = rN -Birth rate: B -Death rate: D Population size: N Time: t -Per capita birth rate: b = B/N -Per capita death rate: d = D/N -Per capita growth rate: r = b - d Intrinsic rate of increase: rmax (unlimited food and shelter, no predators, parasites, or disease, and a comfortable abiotic environment → per capita birth rate is very high, the per capita death rate is very low, and the per capita growth rate is as high as it can be)

Define the following: Cryptic coloration Aposematic coloratino Batesian mimicry Müllerian mimicry

-Cryptic coloration: coloration that allows an organism to match its background and hence become less vulnerable to predation or recognition by prey -Aposematic coloration: bright, contrasting patterns that advertise the unpalatability of poisonous or repellant species -Batesian mimicry: the form of defense in which a palatable or harmless species resembles an unpalatable or poisonous one -Müllerian mimicry: a form of defense in which two or more unpalatable species share a similar appearance

Define density-dependent and density-independent population regulation and list mechanisms for each

-Density-dependent population regulation: factors' influence increases or decreases with the density of the population, logistic model includes the effects in its assumption that per capita birth and death rates change with a population's density. Mechanisms - crowding, intraspecific competition, predation, parasitism and disease -Density-independent population regulation: reduce population size regardless of its density, DOESN'T regulate only reduces (because doesn't cause population to fluctuate, it just cuts it). Mechanisms - global warming, fires, earthquakes, storms, natural disasters

Define the equilibrium theory of island biogeography and the roles of extinction rate, colonization rate, island size, and distance from the mainland

-Equilibrium theory of island biogeography: A hypothesis suggesting that the number of species on an island is governed by a give and take between the immigration of new species to the island and the extinction of species already there. (predicts a number of individuals--not the individuals--that'll be maintained-ish with a constant turnover) -Role of extinction rate: increases as more species are on the island (more competition/chances to die) -Role of colonization rate: high when not much is on the island, declines when a lot on island (most species there already) -Role of island size: large islands have a larger immigration size and lower extinction rate (more room/resources) so have more species/numbers -Role of distance from mainland: islands closer to the mainland have a larger immigration rate (dispersing organisms land closer than further) and distance doesn't affect extinction rates so islands closer to the mainland have more species/numbers

What is the evidence for global warming? Describe shifting geographic range and shifting phenology as a result of global warming.

-Evidence: combustion of fossil fuels and wood produces CO2 as combustion product (emissions increased 29% between 2000 and 2008), greenhouse gases have been increasing since the 1950s (zigzag increase w plant growth in northern hemisphere--photosynthesis removed CO2--each point increasing), atmospheric CO2 increased 35% in the last 150 years and 15% in the last 30 years, average global surface temperature increased more than 0.7°C during the twentieth century -Shifting geographical range: as it gets hotter, species have to move where they live up hills/mountains to get to cooler places (that are their original temperatures) -Shifting phenology: phenology is the timing of annually recurrent biological events (spring blossoming, fruit development, leaf colouration), and as the temperature changes the timing of these events changes

Define the following: food web primary producers primary consumers secondary consumers tertiary consumers omnivores detritivores decomposers predation on food web competition on food web

-Food web: a set of interconnected food chains (portrait of who eats whom with arrow from food to consumer following energy flow) with multiple links -Primary producers: the first trophic level, usually some small plant autotroph -Primary consumers: the second trophic level, usually some herbivore heterotroph that feeds on the primary producer -Secondary consumers: the third trophic level, usually some carnivore heterotroph that feeds on the primary consumer -Tertiary consumers: the fourth trophic level, usually some carnivore heterotroph that feeds on the tertiary consumer -Omnivores: can feed on multiple trophic levels at once -Detritivores: a separate trophic level, extract energy from the organic detritus from other levels, scavengers like earthworms and vultures that ingest dead organisms, digestive wastes, and cast-off body parts such as leaves and exoskeletons, reduce organic material to small inorganic molecules that producers can assimilate. -Decomposers: small organisms like bacteria and fungi that feed on dead or dying organic material, reduce organic material to small inorganic molecules that producers can assimilate. -Predation on food web: one animal eating another -Competition on food web: two animals eating one other

Define the following and explain how they can be tested for: fundamental niche realized niche

-Fundamental niche: the range of conditions and resources that it can possibly tolerate and use -Realized niche: the range of conditions and resources that it actually uses in nature, smaller than fundamental niches, partly because all tolerable conditions are not always present in a habitat, and partly because some resources are used by other species Plot their fundamental and realized niches with respect to one or more resources, and if the fundamental niches of two populations overlap, they might compete in nature.

Define GPP and NPP

-Gross Primary Productivity (GPP): rate at which producers convert solar energy into energy, kcal/m2/yr OR g/m2/yr -Net Primary Productivity (NPP): GPP - respiration, kcal/m2/yr OR g/m2/yr

What are three ways understanding ecological interactions can benefit humans?

-Help governments anticipate the need for social services such as schools and hospitals -Allows conservation ecologists to develop plans to protect endangered species -To predict a population's future growth

What is a keystone species? How does it relate to the Pisaster starfish?

-Keystone species: those that have a greater effect on community structure than their numbers might suggest Pisaster starfish: feeds on California mussels (Mytilus californianus), which are the strongest competitors for space in rocky intertidal habitats Paine removed Pisaster from caged experimental study plots, but left control study plots undisturbed. 10 years later there was an increase in California mussel populations (outcompeted everything else) in the experimental plots as well as complex changes in the feeding relationships among species in the intertidal food web. The overall effect of removing Pisaster, the top predator in this food web, was a rapid decrease in the species richness of invertebrates and algae. By contrast, control plots maintained their species richness over the course of the experiment. Predation by the sea star Pisaster ochraceus maintains the species richness of its prey by preventing mussels from outcompeting other invertebrates and algae on rocky shores.

Define a metapopulation and explain how distance and size affects the likelihood that a patch will be occupied

-Metapopulation: a group of neighboring populations that exchange individuals -as a patch gets more isolated, it is more likely to be occupied -as a patch gets smaller, it is more likely to be occupied

Describe the nitrogen cycle. What is the most abundant/unusable form, what is nitrogen fixation and what organisms do it, what is denitrification and what organisms do it?

-Nitrogen cycle: nitrogen atmosphere to earth by precipitation, in soil it hits bacteria and nitrogen-fixation to ammonia, nitrification to nitrite, nitrite to nitrate, plants absorb nitrate via assimilation, rest of nitrates denitrify it back to N2, decomposers break down waste into nitrogen via ammonification -Most abundant/unusable atmospheric nitrogen form: molecular nitrogen N2 -Role of nitrogen fixation: bacteria convert N into compounds primary producers can use in proteins & nucleic acids, molecular nitrogen (N2) converted to ammonia (NH3) and ammonium ions (NH4) -Nitrogen fixation organisms: bacteria, cyanobacteria, water fern, lightning, volcanic action -Role of denitrification: under low oxygen availability, bacteria converts nitrites or nitrates into nitrous oxide (NO2) and then into molecular nitrogen (N2), that goes into the atmosphere, depletes soil nitrogen in waterlogged or poorly aerated environments (bogs and swamps) -Denitrification organisms: Thiobacillus denitrificans, Micrococcus denitrificans, and some species of Serratia, Pseudomonas, and Achromobacte, Pseudomonas aeruginosa

What are the assumptions of Hardy-Weinberg equilibrium, and what happens if they are violated?

-No mutation -Single population -Large population with no genetic drift -No natural selection -Panmixis (random mating of individuals) If the assumptions are violated, then the population is not in Hardy Weinberg equilibrium. For sake of this class, if P < 0.0001 (Chi Square Test) then we reject it. If there is a 10% difference or more between observed and expected genotype numbers then we will also reject it. This could mean that the population is subdivided, that there is nonrandom mating, and/or there is natural selection.

How can vicariance be tested by the following: phylogeny fossils molecular clocks

-Phylogeny - of species should match when continents break apart and recollide, in order to reject vicariance the phylogeny needs to not make sense when broken apart -Fossils - if older soil levels had fossils spread out, but then newer soil levels only had them in one place???, should be consistent with continental drift -Molecular clocks - the taxa should be older than the split between the two continents

What are the differences between prokaryotes and eukaryotes?

-Prokaryotes (bacteria & archaea) - don't have a nucleus, usually much smaller, higher metabolic rate, higher growth rate, shorter generation time -Eukaryotes (plants, some protists) - have a true nucleus

How can you use rock strata to determine the age of fossils?

-The highest rock strata is the newest/youngest/most recent fossils -The lowest rock strata is the oldest fossils -If you know the age of one layer, it can help you guestimate the rest

What is a trophic cascade? Describe what happened with the orca/otter/urchin/kelp.

-Trophic cascade: predator-prey effects that reverberate through the population interactions at two or more trophic levels, a change is made in the top predator that affects the rest of the food web (e.g. increase 3° consumers, decreases 2° consumers, increases 1° consumers, decreases 1° producers) Orca/Otter/Urchin/Kelp: primary producer = kelp, primary consumer = sea urchin, secondary consumer = sea otter, tertiary consumer = orca, orca started hunting otters at some point in time (they hadn't before) and decreased their numbers 5x, therefore there were less otters to eat urchins so urchins increased 6x, therefore there were more urchins to eat kelp so kelp decreased 10x

What are the three types of survivorship curves?

-Type 1: high survivorship until later in life when mortality takes a toll, large animals with few young and extended care -Type 2: relatively constant rate of mortality in all age classes, a pattern that produces steadily declining survivorship, lizards, songbirds, small mammals -Type 3: high juvenile mortality, followed by a period of low mortality once the offspring reach a critical age and size, plants, insects, marine invertebrates, fish

What is virulence and how do horizontal and vertical transmission affect its evolution?

-Virulence: the negative effect of a disease on a host's fitness, assume that within a host the most virulent strain is the one with the most fitness AND that more virulent strains decrease a host's fitness faster transmission = greater virulence = horizontal transmission = viruses are transmitted among individuals of the same generation slower transmission = lower virulence = vertical transmission = viruses are transmitted from mothers to their offspring

Define population bottleneck and give an example

-a few individuals are randomly (e.g. natural disaster) selected to live, there is a decrease in genetic diversity, the small group that survived passes on its traits -Northern elephant seals hunted to 20 individuals in 1900s

Define the founder effect and give an example

-a few individuals move to a new place, there is a decrease in genetic diversity, they pass on their traits -1774 the Amish moved and Ellis-van Crevald syndrome became very common (dwarfism)

Define species selection. What is the difference between it and natural selection within a species?

-a species with specific characteristics proliferates because of the consequences of speciation or extinction rates -natural selection favors one character in each species, species selection favors a whole species???

List some examples of phenotypic change that are not caused by evolution

-flamingos pink or white bc of the food they eat -humans being tan or pale bc sun

What is the role of sunlight and photosynthesis on plant biomass, the grazing food web, and the detrital food web?

-increases the plant biomass -increases the resources for the grazing food web, increasing those animals -increases the shit that grazers will have, increasing the amount of grazers that will die

When did the KT extinction occur? What went extinct? What is evidence for it? What happened to mammal diversity?

-occurred ~65 MYA -dinosaurs went extinct -a meteor impact caused the extinction due to a large amount of iridium in the geologic record (Iridium is uncommon on earth, but very common in asteroids) -mammal diversity spiked following the impact

What are the four necessary requirements for natural selection?

-phenotypic variation -heritable phenotypic variation -individuals vary in fitness -phenotypes affect fitness

Define and give examples of convergent evolution. How are Eutherian and Marsupial mammals examples of it?

-the kind of evolution where organisms evolve similar (analogous) structures or functions in spite of their ancestors being dissimilar or unrelated -complex eyes in vertebrates & cephalopods streamlined body shape of dolphins & sharks evolution of echolocation in whales and bats paired shell shape of bivalve mollusks & brachiopods -placental mammals + all extinct mammals more closely related to living placentals (humans) than marsupials (kangaroos); whales, elephants, shrews, armadillos, dogs, cats, sheep, cattle, horses -kangaroos, wallabies, koalas, wombats, tasmanian devils, possums

A geologist dates the age of a volcanic rock using an isotope that has a half-life of 30 million years. The geologist finds that for every 500 parent isotopes there are 500 atoms of the break-down product. Approximately how old is the rock?

30 million years

What's net primary productivity if GPP = 25k, 20k used for respiration, and 2k into detrital? How much energy from productivity goes into the grazing food web?

5k 3k

What is the number of species and the lifestyle of the Apicomplexa? What is the common name of the famous Apicomplexa Plasmodium? Where do the haploid and diploid stages occur?

> 4,000 species, all parasites of animals Malaria parasite = good example of apicomplexa Has a complex life cycle (has a haploid & diploid & asexual & sexual)Mosquito bites human → infects it w liver then lungs then RBCs → now diploid & microgamete goes into macrogamete & develops → haploid cycle bc bites & puts haploid back into human

Explain the alleles, genotypes, and phenotypes of the human ABO blood group

AB accepts A, B, AB, & O O accepts O

Explain how the Philadelphia chromosome is a cause of cancer

ABL gene - controls cell growth, after fusion it makes more tyrosine kinase, it causes blood cancer and when overexpressed will cause leukemia, really ****s shit up when translocated with/on BCR Wikipedia says: Aka the Philadelphia translocation, an abnormality in chromosome 22 of leukemia cancer cells, caused by reciprocal translation of genetic material between chromosome 9 and 22, contains the fusion gene BCR-ABL 1, ABL1 gene of chromosome 9 is juxtaposed onto the BCR breakpoint cluster region of chromosome 22, and codes for a hybrid tyrosine kinase signaling protein that is always on and causes the cell to divide uncontrollably

In what direction are DNA nucleotides added?

Added 5' to 3' of the strand on which they are attached, but added 3' to 5' if you are looking at their template

What are the advantages and disadvantages to using fossils as a source of data?

Advantages -only way to know what organisms/phenotypes existed at a specific location at a specific point of time 1000s of years ago Disadvantages -only 1 point in time so can't tell when something appeared or went extinct -incomplete -spatial/temporal bias -preservation bias

What is the phenotypic effect of the bar-mutant in Drosophila?

All of the genes in section 16A duplicated because during crossing over, 2 identical homologous points weren't crossed over, so then there was a duplicate of a specific gene on the chromosome. A bar mutation has both (2 copies), and a deletion has none (no copies). This has strong phenotypic effects and really ****s with their eyes.

Define and give examples of the following: allopatric speciation sympatric speciation

Allopatric speciation -occurs when populations are geographically separated -Darwin's finches w Galapagos islands Sympatric speciation -occurs within a population distributed across a geographic area -two kinds of orcas in the Pacific Ocean

How do density-dependent and density-independent factors play a role in the lives of Alpine Ibex?

Alpine Ibex are density dependent because when there is less snow there are more ibex and vice versa.

Main message of Tomlins et al? What did they hypothesize? What did they do?

Androgen can lead to higher rates of gene expression. However the genes they studied are typically linked with prostate cancer, so using androgen blockers lowers the amount of gene expression and can be used to prevent cancerous gene expression. Hypothesis: ERG gene fused with TMPRSS2 on chromosome with most of ERG's chromosomes; if you take this promoter region you can overexpress ERG gene, promoter from TMPRSS2 makes expression of ERG susceptible to androgens Fluoresence in situ aybridization (FIDH) -- ETV1 - red, TMPRSS2 - green; basically they tagged shit with colors and saw ETV1 & TMPRSS2 equally when healthy BUT in VCaP cells the green & red shows on the same chromosomes (not on different anymore) → concluded that fusion leads to overexpression, also saw that in cancerous cells, some ETV1 genes expressed more

Describe the relationships between genetic drift, population size, the rate at which alleles are lost from a population, and the amount of genetic diversity in a population.

As population size decreases, the rate at which alleles are lost increases, and genetic diversity decreases

Define the two types of polyploid speciation

Autopolyploidy - spontaneous doubling of chromosomes (2n = 6 → 2n = 12 → 4n = 12) Allopolyploidy - hybridization causes doubling (or more) of chromosome number (2n = 6 → n = 3 → 2n = 6) Fun fact polyploidy is more common in plants, less in invertebrates

Explain the methods, results and interpretations of the Avery et al. experiment

Avery, McLeod, & McCarty → almost proved DNA over proteins Methods: treat S bacteria to destroy DNA, proteins, or RNA, R used as normal Results: only died when live S or live R & dead S Interpretations: proteins & RNA didn't transform the bacteria

Compare and contrast genetic drift and natural selection

Both result in a dominant trait eventually (usually), but one is because of chance and one is not. Also, over time, natural selection has more of a direct trend, whereas genetic drift is more random and takes a while before, if it ever, results in equilibrium.

How does the capture-mark-release-recapture method work? What are the assumptions? What does it mean if you violate the assumptions?

Capture-mark-release-recapture: # marked initially * (# in 2nd sample/# marked recaptures) Key assumptions -Being marked has no effect on survival -Marked and unmarked animals mix randomly in the population -No migration into or out of the population takes place during the estimating period -Marked individuals are just as likely to be captured as unmarked individuals If being marked has a negative impact on survival, and the species that is marked dies than you would overestimate the population size If animals come in or out, that disrupts the ratio of marked to unmarked, and throws off the population estimation equation If animals are trap happy, after being marked than the population size would be underestimated

Define the following: DNA helicase topoisomerase single-stranded binding proteins primase DNA Polymerase I DNA Polymerase III sliding clamp DNA ligase

DNA helicase - recruited to ori via spectator proteins, unwinds DNA strand, breaks H bonds topoisomerase - cuts DNA phosphodiester bonds, prevents twisting of DNA, reseals bonds, basically helps shit from being a mess, RELIEVES STRAIN single-stranded binding proteins (SSBS) - prevents 2 strands of DNA from pairing again primase - adds RNA primer DNA Polymerase I - Responsible for removing RNA primers in Okazaki fragments, and replacing it with actual DNA DNA Polymerase III - Synthesizes DNA on the 3' end of a RNA primer sliding clamp - protein encircling DNA, binds DNA polymerase to DNA DNA ligase - responsible for joining DNA fragments together by catalyzing the formation of a phosphodiester bond.

Define the biological species concept, give an example, and list its shortcomings

Definition: basically species can interbreed; species are groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups Examples: grey wolves & coyotes can interbreed Shortcomings: "reproductively isolated" -- how much is enough?

Describe the 3 component life cycle of fungi

Diploid to haploid (via meiosis) to dikaryotic (via plasmogamy) to diploid (karyogamy)

How do disruptive selection and mate choice function in the ecological model of sympatric speciation? How are Rhagoletis host races an example of sympatric speciation?

Disruptive selection - selects for the extremes of the spectrum, so heterozygote disadvantage Mate choice - one extreme only mates with that extreme, the other extreme only mates with that extreme How are Rhagoletic host races an example of sympatric? Each fly flew to its own scent, but after crossed most didn't fly to any specific scent → hybrid breakdown

For Watson & Crick's model of DNA, define the following: double-helix shape antiparallel direction of strands distance between bases number of bases in 1 full DNA twist distance of one full twist of the DNA helix

Double-helix shape: 2 sugar phosphate backbones that twist around each other (bases fill in between) Antiparallel direction of strands: 5' → 3' on one side, 3' → 5' on one side Distance between bases: 0.34 nm between 2 base pairs Number bases in 1 full DNA twist: 10 Distance (in nm) of one full twist of the DNA double helix: 3.4 nm

Where in eukaryotes and prokaryotes does transcription and translation take place?

Eukaryote - transcription in nucleus, translation in cytoplasm Prokaryote - transcription in cytoplasm, translation in cytoplasm

How did the experiments on Paramecium demonstrate that competition occurred?

Gause grew Paramecium aurelia and Paramecium caudatum alone and together (maintaining K with broth and elimination of waste). When grown separately, P. caudatum and P. aurelia exhibited logistic growth. Together P. aurelia persisted and P. caudatum was nearly eliminated. Gause formulated the competitive exclusion principle: populations of two or more species cannot coexist indefinitely if they rely on the same limiting resources and exploit them in the same way.

Explain the methods, results and interpretations of the Griffith experiment

Griffith Experiment → didn't prove DNA over proteins Methods: streptococcus pneumonia, S smooth 180° C colonies bacteria, R rough live bacteria, mix n' match & see what kills Results: mice only died when S w live R Interpretations: S transforms R to be virulent somehow

Explain the methods, results and interpretations of the Hershey and Chase experiment

Hershey & Chase → proved DNA over proteins Methods: dye DNA w 35P and proteins with 35S (radioactive isotopes) to track a gene through generations Results: when bacteriophages infect bacteria, the DNA enters the host cell, not the protein Interpretations: DNA is the unit of inheritance

Define the following: hyphae mycellium sporocarps rhizomorphs

Hyphae - each of the branching filaments that make up the mycelium of a fungus Mycellium - vegetative part of a fungus, consisting of a network of fine white filaments called hyphae Sporocarps - multicellular structure in which spores or spore-producing structures are formed, as in many fungi and slime molds; similar in some ferns Rhizomorphs - rootlike aggregation of hyphae in certain fungi

Describe natural selection from wasps and birds on the size of goldenrod galls that are created by the gallmaking fly.

I HAVE NO IDEA

How do researchers use interspecific crosses to identify genes responsible for reproductive isolation? Explain the research that found the odysseus gene is involved in reproductive isolation in Drosophila simulans and D. mauritiana.

I HAVE NO IDEA

Describe all phases of mitosis (nuclear division)

INTERPHASE - 1st and longest stage G1 phase - most cells in this phase at any point in time, DNA is normal diploid number of chromosomes, 1 of the centrosomes is near the nucleus, the nuclear envelope is intact, cell functions and grows, time varies S phase - DNA replicates and chromosomes develop (now double DNA in nucleus), 1 centrosome is near the nucleus, the nuclear envelope is intact, 10-12 hr G2 phase - replication stops (still double the DNA), centrosomes are duplicating, the nuclear envelope is intact, growth and preparation for mitosis and cytokinesis, 4-6 hr *G0 phase - this happens in G1 if the cell is not going to divide (yet), indefinite PPMAT: Prophase, prometaphase, metaphase, anaphase, telophase Prophase - chromosomes condense (rodlike), nucleolus begins to disappear Prometaphase - nuclear envelope degrades, spindles form, kinetochores form and attach to microtubules Metaphase - microtubules move chromosomes to the metaphase plate, spindles are at the midpoint, chromosomes fully condense and shape Anaphase - separase breaks the chromosomes into daughter chromatids and the sister chromatids are pulled to opposite ends of the cell Telophase - the spindle degrades, chromosomes decondense, nucleolus reforms, RNA transcription begins, the nuclear envelope reforms

Why do dominant and recessive alleles evolve at different rates in response to natural selection (for alleles that are beneficial and alleles that are deleterious)?

If an allele is dominant, then it has two genotypes for which it can be expressed, e.g. AA and Aa. However, if an allele is recessive, then it has only one genotype for which it can be expressed, e.g. aa. Therefore, dominant alleles tend to evolve at increased rates, especially if they increase fitness.

Why does speciation appear unlikely given our understanding of mutation and natural selection

If natural selection removes deleterious alleles, how can a mutation that causes reproductive isolation evolve?

What does the ratio of non-synonymous to synonymous mutations mean?

If the ratio of non-synonmous fixed/synonymous fixed ≠ nony-synonymous polymorphic/synonymous polymorphic, then natural selection has occurred. If the ratios are equal, then genetic drift has occurred.

Why do scientists use both experimental and observational data? What are the advantages and disadvantages of both?

If you use both, you have a more accurate representation of whatever answer you are looking for. You can predict it & back it up & repeat. Experiments Advantages: can control factors & figure out exactly what affects what Disadvantages: logistics, you can't just grab 100s of animals & experiment on them, you need time and space Observational Data Advantages: Disadvantages:

What are the effects of nondisjunction in meisosis I?

In Meiosis I, it really ****s shit up. In the end, 2 haploid cells only have 1/2 a sister chromatid, and the other 2 have 3/2 a sister chromatid.

What are the effects of nondisjunction in meiosis II?

In Meiosis II, it ****s shit up but a little bit less so. In the end, 2 haploid cells have 1 sister chromatid, 1 has 3/2 a sister chromatid, and the other has 1/2 a sister chromatid.

Explain the trp operon

In the absence of tryptophan in the medium, tryptophan must be made. In this scenario, the Trp repressor is inactive, which enables RNA polymerase to bind to the promoter and transcribe the structural genes for the tryptophan biosynthesis enzymes. In the presence of tryptophan in the medium, that tryptophan can be used for protein synthesis, so there is no need for the cell to make tryptophan. Tryptophan binds to the Trp repressor, activating it. The active repressor binds to the operator, thereby blocking RNA polymerase from binding to the promoter. Transcription of the structural genes does not occur.

How has the complex life cycle (haploid vs diploid) changed through the evolution of plants?

Increase in the role of the diploid life stage, diploid = sporophyte, haploid = gametophyte

Explain the conditions where defenses are inducible or fixed, and the test to fiugure out which one it is

Inducible: defenses expressed when a predator is present Fixed: this defense is and always was there Test: induction phase when there is a predator cue and when there is not, fitness phase when there is a predator there and when there is not, graph survival vs risk of predation and see when it was and wasn't expressed

How does heterozygote advantage affect evolution, and how does it relate to sick-cell anemia in humans?

It results in an increased amount of heterozygotes, aka heterosis. With sickle-cell anemia in humans, HbA HbA don't have sickle cell but can die of malaria, HbS HbS have sickle cell but can't get malaria, and HbA HbS have sickle cell trait and therefore don't have sickle cell and are resistant to malaria (the malaria is unable to bind to the sickle cell).

What is the relationship between phosphorus and the recent algal blooms in Lake Erie?

Lake Erie's algae blooms are caused by runoff pollution. This type of pollution occurs when rainfall washes fertilizer and manure spread on large farm fields into streams that flow into Lake Erie. Dissolved, or "bioavailable" phosphorus, easily feed algae in the shallow, relatively warm waters of western Lake Erie. The blooms produce cyanobacteria, or blue-green algae, which in turn makes the liver toxin microcystin, which can harm humans and wildlife.

Describe all phases of meiosis (recombination, from 1 diploid to 4 haploid)

MEIOSIS I Prophase- diploid (2n), DNA condense into threadlike structures, crossing over happens, centrosomes migrate to opposite ends of the cell, nuclear envelope is intact Prometaphase - DNA chromosomes are in tetrads (sister chromatids line up next to each other), kinetochore microtubules connect to chromosomes, nuclear envelope breaks down completely lose nuclear envelope Metaphase I - chromosomes align on metaphase plate, microtubules attach to kinetochores, nuclear envelope is absent Anaphase I - homologous pairs are separated (sister chromatids stay together), kinetochore microtubules facilitate separation (that weird climby thingy), nuclear envelope is absent Telophase I - separates into 2 cells Interkinesis - no new DNA replication, centrosomes are duplicating, nuclear envelope may reassemble or remain absent MEIOSIS II Prophase II - DNA condenses if isn't already, centrosomes migrate to opposite ends of the cell, spindles form, nuclear envelope is absent or present (will disappear if present) Prometaphase II - sister chromatids are together, centrosomes migrate to opposite ends of the cell, nuclear envelope breaks down if it was reformed during interkinesis Metaphase II - sister chromatids align on metaphase plate, centrosomes are on opposite sides of the cell, nuclear envelope is absent Anaphase II - sister chromatids move to opposite ends of the cell, kinetochore microtubules help move sister chromatids, nuclear envelope is absent Telophase II - chromosomes decondense, 1 centrosome per cell, nuclear envelope begins to form around chromatin

Define the molecular clock, what does it assume about the rate of evolution, and what happens if this assumption is violated?

Molecular clock - estimates when two species diverged using the rate (constant) of evolution Calculate amount of divergence - T = D/2RD = current divergence = # substitutions/# sitesR = rate of divergence Estimate age of nodes - se T = D/2R Assumptions about evolution - evolution proceeds at a constant rate, and can determine the rate What happens if assumptions are violated - I HAVE NO IDEA

What are the three components of microevolution? Define them

Mutation - altered DNA base unit → different gene → passed on to next generation; new raw material Natural selection - favorable heritable changes increase org's chance of survival → favored Genetic drift - random changes in allelic frequencies over time

What is a mutualism? Describe the mutualism between mycorrhizal fungi and plants. What is the difference between ectomycorrhizal fungi and endomycorrhizal fungi?

Mutualism: +/+ both populations benefit Mutualism between mycorrhizal fungi & plants: mycorrhizae are fungi that grow alongside the roots of many plant species, they facilitate the plants' uptake of nitrogen and phosphorus from the soil, and the plants provide the fungi with carbohydrates in return Difference between ectomycorrhizal fungi & endomycorrhizal fungi: Ectomycorrhizal fungi: into roots but not into cells Endomycorrhizal fungi: into plant cells, make things that grow between cell membrane & wall for faster sugar exchange

Describe, give examples of, and explain the fitness costs of the following: mutualism competition exploitative

Mutualisms: +/+ both populations benefit, the fitness of both increase, swollen thorn-acacia & crematogaster ants (protect tree for food), mycorrhizal fungi & plants, flowering plants & animal pollinators, animals that eat fruit (shit seeds) & the fruit, Rhizobium and leguminous plants, small marine fishes (eat parasites on) & large predatory fishes Competitive interactions: -/- both competing populations lose access to some resources, the fitness of both decrease, barnacle species Exploitative interactions: Predation +/- predators gain nutrients and energy and prey are killed or injured, the fitness of one increases and the fitness of the other decreases Herbivory +/- herbivores gain nutrients and energy and plants are killed or injured, the fitness of one increases and the fitness of the other decreases Parasitism +/- parasites gain nutrients and energy and hosts are killed or injured, the fitness of one increases and the fitness of the other decreases

What happened with the rabbits and Australia and myxomatosis?

Myxomatosis = infectious/fatal rabbit disease (causes swelling/inflammation/discharge around eyes), rabbits are scared of it Rabbits were introduced to Australia with 24 individuals → 10 years later they could harvest a million rabbits and notice no difference → rabbits so numerous they hurt native species because there were 600 million rabbits in the 1950s Australia introduced myxomatosis and 600 million → < 100 million BUT... the mortality rate was highest for rabbits that had never been exposed to it before, and lower and lower (until 50% or less mortality for a few exposures) until eventually in 2 decades the rabbits evolved resistance SO... virulence of myxomatosis was evolved to be lower as the resistance increased

When does a breeding cross show independent assortment, and when does it not?

Non-independent assortment: everyone with long body has red eyes and everyone with short body has yellow eyes Independent assortment: the alleles do not depend upon each other

What is the cause of Trisomy 21 (Down syndrome)?

Nondisjunction I or II in chromosome 21 during meiosis.

Define and explain the consequences of the following: nonsense mutation missense/non-synonymous mutation silent/synonymous mutation Frameshift mutation

Nonsense mutation - change to stop codon in the protein-coding region → harmful missense/non-synonymous mutations - change in amino acid within the protein → good or harmful silent/synonymous mutations - no change in amino acid bc of degeneracy → no effect Frameshift mutations - alters reading frame bc ignored 1 codon letter, change whole sequence of amino acid in protein → probably pretty harmful

Define the following: one-gene one-enzyme hypothesis one-gene one-polypeptide hypothesis central dogma codon start codon stop codon

One-gene, one-enzyme hypothesis - each gene is responsible for producing a single enzyme that affects a metabolic pathway One-gene, one-polypeptide hypothesis - each gene is responsible for producing a single polypeptide (also proteins & functional molecule) Central dogma - 2 steps, transcription & translation, by which gene info goes to proteins (DNA → RNA → protein) Codon - 3 nucleotide sequence that makes a genetic code unit in DNA/RNA Start codon - AUG methionine, signals to start transcription by ribosome Stop codon - UAA, UAG, UGA, signals to end transcription by ribosome

How does the role of the atmosphere differ in the phosphorus cycle from the nitrogen cycle?

Phosphorus compounds lack a gaseous phase so it is a sedimentary cycle and not in the atmosphere (it uses the earth instead, no gaseous stage)

What are the components of a polysome and what do they do?

Polysome aka polyribosome aka ergasome - RNA molecule + ~2 ribosomes that make RNA instructions into polypeptides, there are free and membrane bound ones, they are between the small and largeribosomal subunits, basically just multiple ribosomes attached to 1 mRNA so that they are all undergoing translation at the same time

Define the following: population size population density population dynamics random dispersion clumped dispersion uniform dispersion

Population Size - number of individuals in a population at a specified time Population Density - number of individuals per unit area or per unit volume of habitat Population Dynamics - how the characteristics of populations change through time and vary from place to place Random Dispersion - organisms are distributed unpredictably/randomly, has a formal statistical definition that serves as a theoretical baseline for assessing whether organisms are clumped or uniformly distributed Clumped Dispersion - with individuals grouped together Uniform Dispersion - organisms evenly spaced in their habitat

Define the following: porifera radiata lophhotrochozoa ecolysozoa deuterostomia When did the following occur? spiral cleavage radial cleavage

Porifera = sponge Radiata = jellyfish, crustacean Lophotrochozoa = mollusc, cuttlefish, annelid Ecolysozoa = arthropod, flatworm, centipede Deuterostomia = vertebrate, echinoderm, starish, noncordate Spiral cleavage (blastula into mouth) evolved right before node into lophotrochozoa & ecolysozoa Radial cleavage (blastula into anus) evolved right before deuterostomia

What were the predictions of the oral polio vaccine hypothesis for the emergence of HIV, how was phylogeny used to test this prediction, and was the oral polio vaccine hypothesis supported or refuted?

Predicted that Pan troglodytes schwinfurthii, used to make the vaccine, were infected somehow in the lab Polio originated in the 1950s in West Africa though, and when build a phylogeny of troglodytes vs schwinfurthii, HIV/AIDs is not linked to the schwinfurthii refuted

Describe the simple predator-prey model

Prey peaks before the predator, it's an interspecific density dependent interaction, similar to fox-hare Basically, the number of prey goes up, now the predator has more to feed on, the number of predators goes up, the number of prey goes down, now the predator has less to feed on, the number of predators goes down, the number of prey goes up, etc. To test it, take out the predators, and if the survival drop for prey almost completely is gone, this is probably the right model

Define and give examples of the following: prezygotic isolation postzygotic isolation

Prezygotic isolation -when reproduction between individuals is prevented by factors operating before fertilization -habitat isolation, behavioral isolation, temporal isolation, mechanical isolation, gametic isolation Postzygotic isolation -when reproduction between individuals is prevented by factors operating after fertilization -hybrid offspring are infertile

How does mRNA splicing work and what is its purpose?

Process: snRNPs (small nuclear ribonucleoproteins) + pre-mRNA + proteins = spliceosome = large RNA-protein molecular complex; forms intron in mRNA into a lariat (noose shape) and cleaves it Purpose: removes introns & joins exons to make mRNA that will make the right protein

What are the locations and roles of the following: promoter gene transcription unit transcription factors polyadenylation signal RNA polymerase II

Promoter Location: on DNA near 5' at start Role: tells RNA polymerase where to start/at what strand Gene Location: segment on DNA (promoter is at the start of it) Role: be template for RNA to copy Transcription unit Location: segment on DNA (start to stop) Role: be template for RNA to copy Transcription factors Location: on promoter, RNA polymerase binds to them Role: helps RNA polymerase bind & function Polyadenylation signal Location: tail of mRNA Role: ends mRNA strand RNA polymerase II Location: along DNA Role: catalyzes DNA → RNA transcription

Define the following and tell where they evolved on a phylogeny: protostome deuterostome

Protostome - 4 cells to 8 cells, 1st mouth made, Deuterostome - 4 cells to something but he clicked through the slide too quickly, 1st anus made

Define the following and tell where they evolved on a phylogeny: radial symmetry absent symmetry bilateral symmetry

Radial symmetry - symmetry no matter which way cut the animal in half, on one branch coming from eumetaria, 2ndary evolution of some starfish to have radial symmetry before deuterostomia Absent symmetry - no symmetry Bilateral symmetry - only symmetry when cut in half one way, on the other (proto/duetero) branch coming from eumetaria

Explain the rationale for the McDonald-Kreitman test

Rationale: The idea is that silent substitutions occur more rapidly than replacement substitutions. And according to the neutral theory, replacement substitutions should = silent substitutions throughout time. Therefore, replacement : silent substitutions :: nonsynonymous : synonymous polymorphisms within species (the latter two should be equal throughout time as well). The test states that if there are more fixed mutations (whether nonysnonymous or synonymous), then every individual has them and as a result, it is more neutral and that trait was controlled by genetic drift. It also states that if there are more polymorphic mutations (whether nonsynonymous or synonymous), then some individuals have one version while other have another and as a result, it is more polymorphous and that trait was controlled by natural selection. Example: Fixed Polymorphic Non-synonymous 7 2 Synonymous 17 42 29% (7/(17+7)*100) of the fixed differences are replacement substitutions (nonsynonymous), but only 5% (2/(2+42)*100) of the polymorphic differences are replacement substitutions (nonsynonymous). Therefore, the neutral hypothesis doesn't apply here and one fixed mutation is more advantageous so natural selection is occurring here (because if it wasn't then the percentages would be equal).

How do you calculate observed allele and genotype frequencies?

Say gene "A" has 2 alleles, A1 and A2. 3 possible genotypes, A1 A1, A1 A2, A2 A2 Observed allele frequencies Frequency of A1 = F (A1) = p Frequency of A2 = F (A2) = q p + q = 1 Observed genotype frequencies Frequency of genotype A1 A1 = F (A1, A1) = p2 Frequency of genotype A1 A2 = F (A1, A2) = 2pq Frequency of genotype A2 A2 = F (A2, A2) = q2

Define and give examples of the following: secondary contact hybrid zones reinforcement

Secondary contact -when allopatric populations reestablish contact after a geographical barrier is eliminated or breached - Hybrid zones -the areas in which, during the early stages of secondary contact (prezygotic reproductive isolation may be incomplete), some members of each population may mate with individuals from the other and produce viable and fertile offspring - Reinforcement -postzygotic isolation evolves before prezygotic isolation -

Define sedimentary rock and volcanic rock

Sedimentary rock - comes from dirt/cement/rock, can't do radiometric dating, can find fossils Volcanic rock - comes from volcanoes, can do radiometric dating, can't find fossils

Describe the components of the ribosome and their function in translation

Small ribosomal subunit - after tRNA attaches to it, it attaches to the mRNA at the 5' cap, it is under the mRNA and moves down in the 3' direction after the large ribosomal subunit attaches, aiding in elongation Large ribosomal subunit - attaches to small ribosomal subunit, has E P A sites to organize translation esp elongation, used tRNA exists in the E site, stuff bonded and fed out in the P site, stuff inserted in the A site

What are the locations and roles of the following: small ribosomal subunit large ribosomal subunit initiator tRNA other tRNAs mRNA initiation factors GTP GDP elongation factors release factor

Small ribosomal subunit - attaches to tRNA & mRNA, moves down w large to aid in elongation Large ribosomal subunit - attaches to small, moves down w small to aid in elongation Initiator tRNA - binds to start codon, attached to methionine, put in P site, helps make up ribosomal subunit Other tRNAs - 1st tRNA is the methionine one for AUG, others carry different amino acids dep. on the codon, they still enter at the A site, bind to the codons, move to the P site, have pep.trans. Attach the polypeptide strand to its amino acid, and move to the E site as the chain is passed on to the next tRNA mRNA - this is what the ribosomal subunit is attached to, this has the sequence of codons & determines what polypeptide will be made, this was made off of the DNA template strand Initiation factors - proteins, bind to small subunit of ribosome in initiation, help form the complex GTP - makes GDP via hydrolysis to power translation, specifically powers binding tRNA to the A site and for moving the ribosomal subunit down the mRNA chain GDP - GTP undergoes hydrolysis to make this, elongation factors bind to this until GTP is needed and then it is released an an exchange occurs Peptidyl transferase - catalyst RNA in large ribosomal subunit, attaches amino acids to each other via peptide bonds Elongation factors - proteins that facilitate elongation by helping make peptide bonds, helps ensure accuracy during translation when everything is happening so quickly Release factor - protein that matches up with the stop codon and signals the polypeptide chain to break off and leave the ribosome (with the help of 2 GTP → 2 GDP)

Given step 1, write the mRNA strand made, codons paired, polypeptides paired, what steps are transcription, and what steps are translation (you may use/google the table of codons/amino acids) Step 1 - template DNA strand: 5' A T G C T G T A G 3'

Step 2 - mRNA strand made: 3' T A C G A C A T C 5' Step 3 - codons paired: 5' A U G C U G U A G 3' Step 4 - polypeptides paired: Methionine leucine STOP Step 1 → 3 = transcription Step 3 → 4 = translation

Define the following: taxa node tip root clade sister clade (or sister taxa) monophyletic group paraphyletic group

Taxa - the organisms included in any category of the hierarchy Node - each branching point Tip - the most recent species Root - most common ancestor of all species included in the tree Clade - evolutionary lineage (node and branches and branchlets and things) Sister Clade (or Sister Taxa) - the two clades/taxa that come from the same node and are side by side Monophyletic Group - 1 clade and all the descendants but no other groups (e.g. Felidae and Animalia, cats and animals) Paraphyletic Group - ancestor and SOME descendants

How do kinetochore microtubules move during mitosis and meiosis and how did the experiment work that determined this?

The experiment was seeing if microtubules retract by looking at the dyed part and seeing if it moved. However it didn't, which meant motor proteins move along the microtubule, pulling the sister chromatids, or chromosomes, and the motor proteins degrade the microtubule as it moves up it. It doesn't destroy the protein to my knowledge

Compare and contrast the trp and lac operons

The lac operon is inducible (positively controlled), meaning that it is normally off, but lac turns it on; the trp operon is repressible (negatively controlled), meaning that it is normally on but trp turns it off.

Describe the experiment with the salamanders and what this said about density-dependent and density-independent factors

The salamander experiment involved 11 natural ponds, each divided in half with a plastic sheet. On one half, the population was reduced (other side was natural density). Over time, more of the salamanders in the reduced population survived, suggesting that the density-dependent factor is possibly limiting the amount of food available (because the salamanders are cannabilistic, so at low densities they don't give a **** about each other, but at high densities they eat each other and are just all around more aggressive.)

Why are life tables useful for ecologists?

They are useful for ecologists because they can monitor different groups of organisms (or of the same organism) and observe changes/differences in survival rates. From here, they can try and fix things for the population that is suffering.

How are steroid hormones involved in gene expression?

This is that WACK shit where a frog gets stressed and shit and then its steroid hormone is like oh shit we gotta release shit to help with all this ****ed shit that's happening so it triggers a bunch of other genes to express their shit to help protect this frog somehow but they woulda never been expressed without the ****ed shit situation in the first place.

Define the wobble hypothesis

This is the idea that the 3rd letter in a codon has more leniency because there is more degeneracy with it. So basically if there is a mutation in the 3rd letter, it is less likely that there will be a mistake in the protein coded for as compared to if there was a mutation with the 1st or 2nd letter.

Explain the Jacob and Monod experiment

This is the lac operon bullshit. They took ß-Galactosidase (not always in the cell ready to break down lactose into galactose and glucose), and added/removed an inducer (saw that more BG made without inducer). Lac subunits Lac Y - makes mRNA for permease (helps bring lactose into E. coli) Lac Z - makes mRNA for BG Lac O - Lac i - not part of BG transcription unit (its mRNA doesn't become BG) PRODUCES LAC REPRESSOR Alleles of gene Lac Z Z+ - normal BG Z- - nonfunctional BG I+ - inducible BG (breaks galactose into glucose and lactose if there's a lot) I- - always makes BG They did an experiment with I-and Z- and no inducer, and then added I+ and Z+ genomes to the E. coli (made it diploid for a bit). Then they had no inducer, then they had an inducer. They found out that the wild type is only made with the inducer, and that the inducer only works on I+.

Describe the research on the duplication of gene RNASE1 into RNASE1b, including recognizing the groups of organisms involved, how it is related to changes in diet, rates of evolution in the duplicated gene, evidence for evolution due to natural selection, and changes in gene function in different contexts.

This research was to find out how you can tell if something evolves from an error way back when. This looked at rhesus monkeys (who eat fruits/insects) and douc langurs (who eat leaves). It examined RNASE (ribonuclease), and noticed that there were high amounts in leaf-eating animals (langurs) to help w fermentation & breaking down bacterial DNA. The RNASE 1 (rhesus) looked like .....T.......F......K........................ The RNASE 1B (langur) looked like .....T.......F......K.....E.......K....... *The E was the one that was only in douc langurs The hypothesis was that RNASE 1B resulted from a duplication in RNASE1, and the evidence for natural selection was done w McDonald Kreitman test, and found that it exists for synonymous. Also, there are different optimal pHs for the rhesus and langur which lets them eat leaves.

What are the 5' and 3' orientations of DNA and RNA throughout transcription and translation?

Transcription DNA: two strands run in opposite directions, so one runs 3' → 5' and the other runs 5' → 3' RNA: made off of the 3' → 5' template strand, so runs 5' → 3' as made Translation: DNA: not really used, mRNA/RNA is used RNA: runs 5' → 3', RNA polymerase moves down in that direction, adding nucleotides as goes

Define the three stages in transcription (initiation, elongation, termination)

Transcription i) initiation - RNA polymerase binds to transcription factors on RNA polymerase ii) elongation - RNA polymerase II separates 2 strands of DNA (template & non-template) & adds mRNA to template DNA strand, nucleotides added by RNA complex iii) termination - RNA polymerase transcribes a terminator/stop codon & ends the mRNA with polyadenylation signal (polyA tail), precursor mRNA cleared

Define transcription and translation

Transcription - RNA polymerase linking nucleotides to make (m)RNA from DNA template Translation - ribosome uses mRNA to make a protein

How do the three stages of transcription (initiation, elongation, termination) in eukaryotes work?

Transcription in eukaryotes i) Initiation - RNA polymerase uses transcription factors to bind to promoter ii) Elongation - RNA polymerase II sep DNA, adds mRNA to template, RNA complex adds nucleotides iii) Termination - polyA signal transcribed into mRNA and is cleared by proteins

How do the three stages of translation (initiation, elongation, termination) in eukaryotes work?

Translation in eukaryotes Initiation - tRNA carrying methionine attaches to small ribosomal subunit, they bind to the 5' GTP cap, they go down the 3' direction and stop at the start codon, the large ribosomal subunit attaches to the small/tRNA and puts the tRNA in the P site and the first codon in the A site, GTP hydrolysis to GDP powers this Elongation - tRNAs bring anticodons (amino acids) to match the codons in the A site, binds to it, then peptidyl transferase (catalyst RNA that attaches amino acids) peptide bonds methionine to the next amino acid & feeds it out the exit tunnel in the P site as the complex shifts one codon down themRNA and the first tRNA disconnects from the E site, GTP hydrolysis to GDP powers this Termination - the release factor (protein) matches up with the stop codon, polypeptide chains break off & leave the ribosome, 2GTP → 2 GDP make the subunits leave, *NB! there are multiple ribosome complexes transcribing this stuff at the same time

Define the following chromosome changes: translocation (reciprocal) inversion duplication deletion

Translocation (reciprocal) - Non homologous chromosomes switch parts of their DNA ****ing shit up because the gene is on the wrong chromosome *this one is because of crossing over in whole chromosomes, not with homologous pairs, but basically it is when some of the DNA is duplicated but not all of it?, e.g. ABCDEFGH & KLMN → ABCDEFGN & KLMFGH inversion - part of the DNA is just flipped, e.g. ABCDEFGH → ABCDGFEH duplication - part of the DNA is just duplicated, e.g. ABCDEFGH → ABCDEDEFGH deletion - part of the DNA is just deleted, e.g. ABCDEFGH → ABCDEGH

When did the following happen? vascular tissue seeds flowers

Vascular tissue - lymphocytes 1st had 'em Seeds - gymnosperms 1st had 'em Flowers - angiosperms 1st had 'em

What was the contribution of Wilkins and Franklin to Watson and Crick's DNA model?

Via x-ray diffraction, they found photo 51 which supported their (W & C's) findings about the structure

Define the following: vicariance dispersal

Vicariance - new barrier appears to explain the global distribution of organisms Dispersal - preexisting geographic barrier to explain the global distribution of organisms

What was Dr. Burn's presentation about?

What makes plants invasive, and how do plant-soil interactions work? Does soil biota influence disease resistance? Her experiment: -Manipulated Phytophthira, it killed plants. -Collected soil and did an experiment with plants with the pathogen & soil microbiome. -Double factorial setup: Sterilized Microbiome w/o Phythophthira, Sterilized Microbiome w/ Phythophthira, Regular Microbiome w/o Phythophthira, Regular Microbiome w/ Phythophthira -Collected soil and did an experiment with plants without the disease and plants with the disease, both with the soil microbiome. The plants without the disease had higher survival. -The soil is disease suppressive, so there is something in the soil that benefits the plants to fight their disease. -Plant type also determines the effectiveness of soil biota for disease suppression, if a plant is very susceptible to disease, than the soil biota is more effective usually

Define the following: Gondwanan distribution Laurasian distribution

When Pangaea broke up, the northern continents of North America and Eurasia became separated from the southern continents of Antarctica, India, South America, Australia and Africa. The large northern continent is called Laurasia and the southern continent is called Gondwanaland.

How does recombination affect evolution, especially with Drosophila?

When you have tightly linked alleles, the chance of having beneficial mutations decreases. When you have recombination though, the rate of adaptive evolution increases. They graphed the non-synonymous substitution rate (y axis dN) versus the recombination rate (x-axis) and saw a general increasing trend, so on average recombination rates and non-synonymous substitution rates are directly proportional. Then they graphed synonymous versus recombination rate and saw no trend; therefore, increasing the recombination rates freezes up the ability of a population to adapt.

How can you use a phylogeny to identify the source of a disease

Whichever group has more in common or is more related to the one with the disease probably is responsible---e.g. HIV/AIDS

What is the approximate frequency of gene duplications in Eukaryotes and bacteria?

Wikipedia says: the mutation rate in unicellular eukaryotes and bacteria is 0.003 mutations/genome/cell/generation EQUALLY COMMON IN PROKARYOTES AND EUKARYOTES

How is parsimony used in caldistic analysis?

You go with the clade that has the least amount of trait/character changes

How are nucleotides added to a growing DNA strand and how does that change the amount of phosphate groups on the DNA?

You have a 5 carbon sugar (deoxyribose), a nitrogenous base (ATCG), and 1-3 phosphate groups. When adding nucleotides, dATP (deoxyadenosine triphosphate) is involved, and 2 phosphate molecules are lost, and hydrolysis converts pyrophosphate to 2 phosphate molecules.

Define a synapomorphy

a shared derived character state among species that provides a clue that they may be members of the same clade

Define the following: autosomes sex chromosomes homogametic sex (what is it in humans and drosophila?) heterogametic sex (what is it in humans and drosophila?)

autosomes - all chromosomes except for sex chromosomes sex chromosomes - any chromosome involved in determining the sex of an organism (XX, XY) the homogametic sex - the sex w 2 copies of the same sex chromosome, (homogametic sex in humans is XX female, homogametic sex in Drosophila is XX female) the heterogametic sex - the sex w 2 different sex chromosomes (heterogametic sex in humans is XY male, heterogametic sex in Drosophila is X male)

How do fitness cost/benefit function in mutualisms, and what happens if the relationship cost/benefit changes for one?

both partners benefit, common, do not require active cooperation (each species exploits the other for its own benefit) If it becomes less beneficial for one, then it gets closer to being an exploitative relationship.

Define evolution

change in allelic/genetic frequencies in populations over generations due to natural selection, mutation, & genetic drift on a graph, genetic drift is random (natural selection is trend)

What are the roles of the following in eukaryotic gene expression: chromatin nucleosome TATA box promoter general transcription factor proximal promoter region transcription complex enhancer activator coactivator transcription initiation site

chromatin - a protein and DNA complex. DNA is more condensed, and chromosomes are made from chromatin. nucleosome - a group of histones (usually 8?) with DNA wrapped around it TATA box - 5'-TATAAA-3' very specific region of the promoter that signals where transcription begins promoter - larger region of noncoding DNA that signals where transcription begins, because of TATA box, and is where general transcription factors bind to. general transcription factor (GTF) - attaches to the TATA box to enable RNA Polymerase III to bind to the promoter proximal promoter region - about 250 base pairs located before the gene that contains primary regulatory elements transcription complex - RNA polymerase + transcription factors enhancer - 50-1500 base pair region bound by activator proteins, increases the likelihood that transcription of a gene will occur activator - a transcription factor protein that increases the rate of transcription of a gene(s) coactivator - a transcription factor protein that binds to an activator transcription factor protein to increase the rate of transcription of a gene(s) transcription initiation site - a location at the 5' end of a strand of DNA at which transcription starts

Define the following: conservative model of DNA replication semi-conservative model of DNA replication dispersive model of DNA replicatikon Meselon & Stahl experiment

conservative - predicts that all of the DNA will come back together (cartoon was both strands blue or both strands red) semi-conservative - predicts that all of the DNA in each strand will come back together (cartoon was one blue one red strand intertwined) dispersive - predicts all of the DNA mixes (cartoon was all blue or red but with blue or red splotches so mixy) Meselon & Stahl - initially raised bacteria in a "heavy" isotope so that all of the DNA would be heavy, then switched to a "light" isotope so that all of the new DNA would be light, then separated DNA by weight to determine grouping of "old" vs "new" DNA, they did this w a centrifuge

Define the following and describe their relationships between phenotype and fitness and how each selection affects the phenotypic mean and variance:

directional selection -shifts the mean phenotype towards the end of the distribution favored by natural selection -one extreme phenotype is better for fitness than the other and the mean -increases or decreases (shifts in one way) the phenotypic mean. Decreases the phenotypic variance (because everything shifts one way) stabilizing selection -favors the mean phenotype over extreme phenotypes -the mean phenotype is better for fitness than either extreme -decreases the phenotypic variance (because everything shifts towards the middle) disruptive selection -decreases the frequency of the mean phenotype, but increases the frequency of extreme phenotypes -both extreme phenotypes are better for fitness than the mean -stabilizes the phenotypic mean (because most on one end and most on another) but doesn't chance very much. Increases phenotypic variance since for phenotypes are different (higher or lower)

Define the following: epigenetics DNA methylation

epigenetics - changes that do not involve alterations in the DNA sequence (basically alterations because change gene expression) DNA methylation - cytosine in promoter region of DNA gets methylated which prevents transcription

Define the following: gene structural gene regulatory gene operon promoter operator inducer activator repressor corepressor positive control negative control

gene - a specific sequence of base pairs in a genome containing the code for a protein molecule or one of its parts, or for functioning RNA molecules such as tRNA and rRNA structural gene - a gene that encodes for a protein other than a regulatory protein regulatory gene - genes that may or may not be expressed, depending on the conditions in which they exist; a gene that encodes for a protein that regulates the expression of a structural gene operon - a unit of genes which regulate genes that synthesize proteins promoter - the region where RNA polymerase initially binds during transcription operator - where the regulatory protein (a protein that affects gene expression e.g. lac repressor) binds inducer - a molecule that causes the transcription of structural genes (in lac, Allolactose is the inducer; it binds to the repressor and prevents the repressor from functioning) activator - a regulatory protein which turns genes on. If the activator is gone or not on, genes will not be expressed. This is a positive control. repressor - a regulatory protein that turns gene expression off. If a repressor is present, genes will not be expressed. This is a negative control. corepressor - a regulatory molecule that activates the repressor, thereby turning off expression, this is what attaches to the repressor and changes its shape

What are sex-linked genes?

genes that are on the sex chromosomes, so how they are inherited depends upon if an organism is a female or male

What is the advantage of sexual vs asexual reproduction?

genetic diversity

Define an outgroup

have all ancestral traits

Define the following: histone acetylation de-acetylation

histone - a group of proteins found in chromatin acetylation - removes the positive charge on the histone tails and makes it so that they are not able to wrap around DNA as tightly, exposing genes for transcription de-acetylation - put the positive charge back on the histone tails and makes it so that they can wrap tightly around the DNA, covering up genes and preventing them from being transcribed

Define the following and explain the cladistic way to construct phylogenies: homologous trait parsimony homoplasy ancestral trait derived trait outgroup synapomorphy

homologous trait - traits that have the same state in multiple taxa because that state was inherited from the common ancestor Parsimony - the simplest explanation that can explain the data is preferred → the hypothesis with the smallest number of character changes (when it comes to analyzing the phylogeny) is the best one Homoplasy - a character shared by a set of species but NOT present in their common ancestor, can sometimes be called a convergence Ancestral trait - a trait that was retained by a species from its ancestor Derived trait - a trait that has evolved since its ancestor Outgroup - a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup Synapomorphy - when two sister taxa have the same trait, as inherited from their most recent common ancestor, but not from the ancestors before that one

What are androgens?

hormones, here they increase gene expression; if binds it will incrase T expression so if have T promoter attached to E promoter what'll happen in these different scenarios (is what the graph is showing), in this graph you are in an environment with no natural androgens

Define the following: linkage map map unit centimorgan

linkage map - a table for a species or population that shows the position of its genes relative to each other in terms of recombination frequency (not position on a chromosome) the genes are arranged with respect to recombination rate, not position map unit (mu) - a unit for measuring genetic linkage, represents 1% on a linkage map it is 1% of the recombination frequency centimorgan (cm) - the same as a map unit, the distance between loci (chromosome positions) where the likelihood of a crossover is 0.01 it is 1% of the recombination frequency

Define mRNA breakdown rate

mRNA breakdown rate - depends upon the half-life of a protein, e.g. casein mRNA, if prolactin is absent it is 5 hours, if prolactin is present it is 96 hours, this is useful for when mammals are nursing their offspring

Define microRNA and describe how it is a kind of post-translation gene regulation?

microRNAs - RNAs that bind to the 3' UTR in the cytoplasm & break it down (or keep it from translation) 1) RNA Polymerase II transcribes miRNA → processed by proteins 2) pre-mi-RNA is exported into the cytoplasm 3) dicer enzyme removes loop from pre-miiRNA hairpins 4) double-stranded miRNA binds to protein complex 5) protein complex degrades 1 miRNA strand 6) miRNA from miRISC binds to target mRNAs in 3' UTR

Define epistasis

one gene affects the expression of another gene (e.g. fur in beach mice)

Define the following: origin of replication replication bubble replication forks leading strand template lagging strand template Okazaki fragment

origin of replication (ori) - the location at which replication will start within a bacteria replication bubble - from one replication fork to the next, includes the whole open section of DNA that is being added to replication forks - the location at which the strands split leading strand template - the top 3' to 5' strand off of which shit is added (added 5' to 3' direction) lagging strand template - the bottom 5' to 3' strand off of which shit is added (added 5' to 3' direction and has to keep going back) Okazaki fragment - the DNA in between the RNA primers (the different sections that the lagging strand has that have to be knitted back together)

What is the endosymbiotic theory and how does it relate to mitochondria and chloroplasts?

original prokaryotic host cell → multiple invaginations of the plasma membrane → bacteria become mitochondria → photosynthetic bacteria become chloroplasts

Define the following: phenotype gene allele dominant traits recessive traits incomplete dominance codominance

phenotype - an organism's traits gene - a sequence of DNA containing code for a protein or functioning RNA allele - different versions of a gene (e.g. A1, A2, Aa, etc.), diploid organisms have 2 alleles per gene dominant traits - the trait is expressed either in homozygous or heterozygous form recessive traits - the trait is only expressed in homozygous form incomplete dominance - the heterozygous phenotype is in between the different homozygous ones (e.g. pink not red or white) codominance - both alleles have approximately equal effects (e.g. blood type for humans, AB isn't one or the other, it is both)

Define the following: ploidy diploid homologouos chromosomes sister chromatids karyotype

ploidy - the number of chromosome sets (e.g. humans are diploid bc we have 2 sets of each chromosome → 23 chromosome sets → 46 chromosomes) diploid - the organism has 2 sets of each chromosome (2n, VERY common in eukaryotes) haploid - the organism has 1 set of each chromosome (1n, e.g. fungi) homologous chromosomes - the chromosomes that make up a set (e.g. with diploid humans, there's a set for each of the 23 chromosomes, 1 from the mom and 1 from the dad, each pair is a pair of homologous chromosomes) sister chromatids - 2 identical copies of each chromosome, they get separated during division but before that cohesins hold them together in "sister chromatid cohesion", think >< → > & < karyotype - a complete set of metaphase chromosomes arranged by size and centromere position, this identifies different species

Define positive and negative control. What will happen if the regulatory gene in these environments stops working?

positive control - where a protein is present that turns gene expression on negative control - where a protein is present that turns gene expression off If the regulatory gene in a positive control environment gets ****ed, then the process will just never occur. If the regulatory gene in a negative control environment gets ****ed, then the process will just never stop occurring.

Define the following: pre-cursor mRNA mRNA 5' UTR 3' UTR 5' cap polyadnylation signal poly(A) polymerase poly(A) tail intron exon

precursor-mRNA - 5' cap -- UTR -- exons -- introns -- exons -- UTR -- polyadenylation signal/polyA tail -- UTR -- 3' cap; the RNA strand copied from the DNA template before certain parts spliced out mRNA - the strand made from the DNA template strand, includes uracil; used to build protein polypeptide chains 5' UTR - untranslated region after the 5' cap & initiator codon; modulates mRNA transport, helps w stability, helps w subcellular localization, helps w efficiency of translation 3' UTR - untranslated region before the 3' cap & after the teminator codon, includes the polyA signal; has regulatory regions that influence gene expression after transcription 5' cap - 7 methylguanosine cap, at the beginning of the mRNA, added during elongation; protects mRNA from degradation, helps ribosome bind in translation Polyadenylation signal - in the 3' UTR section; signals for the Poly (A) polymerase to add a polyA tail Poly (A) polymerase - polynucleotide adenylyltransferase; adds the polyA tail at the end of the mRNA Poly (A) tail - 100-250 residues long, added to 3' end of mRNA; protects the mRNA from degradation, helps w transcription termination, helps export mRNA from the nucleus, helps w translation Intron - non-protein coding parts of the mRNA, they are gotten rid of my snRNPs Exon - protein coding parts of the mRNA

Define the following: proofreading mismatch repair excision repair

proofreading - when DNA polymerase adds incorrect nucleotides to growing DNA, the DNA polymerase reverses, removes the shit nucleotide, and adds the correct nucleotide mismatch repair - corrects errors missed by proofreading, about 1 error/million nucleotides/replication, it fixes shit by cleaving the DNA on either side with the mismatch repair protein, it removes the shit DNA & replaces it & DNA ligase seals the gap (aka nick) excision repair - repair of DNA damage, it removes and replaces the damaged nucleotide (e.g. dimer 2 - bonded together that shouldn't be, or radiation/chemicals that ****s with the DNA)

Define homology

similarity of the structure, physiology, or development of different species of organisms based on their descent from a common evolutionary ancestor

Define the following: spindle poles kinetochore kinetochore microtubules

spindle poles - the things the spindles extend from, this is the ovals that are 90° to each other kinetochore - proteins associated with the centromere of a chromosome during cell division, to which the microtubules of the spindle attach kinetochore microtubules - microtubules that extend from the centrosome to the kinetochore

Define the following: telomeres telomerase

telomeres - repeated sequences of nucleotide bases, typically lost when RNA primer is deletes, chromosomes shrink with each mitotic cycle telomerase - prevents shortening of telomeres, expressed in a few cells, by adding noncoding nucleotides to the telomeres to prevent loss of genes.

Define the following: test cross monohybrid crosses dihybrid crosses

test cross - cross between a wild type individual and a homozygous individual so that you can find out the phenotype of the wild type individual (homozygous or heterozygous) monohybrid crosses - cross between two individuals that are each heterozygous for alleles of one gene (e.g. think of your normal cross w Aa x Aa) dihybrid crosses - cross between two individuals that are each heterozygous for alleles of two genes (e.g. think of the fruit fly cross w BE Be EB Eb x BE Be EB Eb)

Explain the lac operon

the lac operon is inducible (so the hormone turns it off but lac turns it on, this was studied in E. coli). If there's lactose, allolactose will be made which will bind to the repressor and make it not repress anymore

Define polygenic trait

the phenotype of a trait is determined by multiple genes, height and skin color are good examples of this because there is a continuous distribution of them, it doesn't follow the same phenotypic ratios of Mendel, aka multifactorial

Define an area cladogram

used to represent a hypothetical relationship between groups of animals, made with lines, nodes are where the lines cross, lines represent evolutionary time or a series of organisms that lead to the population it connects to

Define phylogeny

used to test evolution hypotheses, study origin/spread of disease, predict harmful/beneficial traits; basically the trees n' shit that show how a thingy evolves; the closer taxa are to each other, the more related they are; evolutionary history of organisms

Define genetic drift

variation in relative frequencies of different genotypes in a small population bc particular genotypes can disappear when individuals die/don't reproduce