BIO311D FINAL EXAM

1-1.  Compare and contrast mitosis and meiosis in terms of their function and the chromosome number in daughter cells as compared to the original cell. 

__mitosis__

* identical replication
* asexual
* same number of chromosomes

__meiosis__

* produces gametes
* reduction division (1/2 the number of chromosomes)
* sexual

1-4. Describe how genetic variation among individuals is generated by meiotic independent assortment and by recombination during crossing over. Be able to label and follow alleles on chromosomes

__independent assortment__

* homologous chromosomes align (differently - during metaphase 1 - is what creates variability)
* separate into 4 daughter cells at random creating new combinations of alleles.
* produces 2^n combinations

__crossing over__

* homologous chromosomes exchange DNA segments in prophase 1 of meiosis
* forms hybrid chromosomes of the OG homologous chromosomes that contain new combinations of alleles

1-5. Distinguish asexual reproduction from sexual reproduction, and state the functions of meiosis and fertilization in sexual life cycles.

__asexual__

* one individual produces genetically identical offspring to them
* mitosis (not meiosis)
* allows for rapid colony and adaptation to changing environments, and lacks diversity.  

__sexual__

* requires two individuals (male’s sperm and female’s egg) for the gamete fusion to produce an offspring with a combination of both genetics
* meiosis will make gametes for reproduction.

1-8.  Generate Punnett squares and predict the ratio of offspring genotypes and phenotypes when given information about parental phenotypes and the dominance pattern.

we know how to do that :)

1-16. What is the genetic (chromosomal) basis of sex determination in mammals?

* X and Y chromosomes
* Y containing the sry gene coding for the testis-determination factor protein.

1-18  Given information about parental phenotypes for an X-linked recessive trait, draw a Punnett Square (including X and Y chromosomes) and predict the percentage or fraction of (a) their offspring and (b) their sons that would express the recessive trait in their phenotype.

we can do that :)

1-22. Calculate allele frequency (p, q) and genotype frequencies (p2, 2pq, q2) using the __two__ Hardy-Weinberg equilibrium equations.

* p + q = 1
* p = dominant phenotype %
* q = recessive phenotype %
* p^2 + 2pq + q^2 = 1
* p^2 = homozygous dom
* 2pq = heterozygotes
* q^2 = homozygous recessive

1-23. Name the main assumptions of Hardy-Weinberg equilibrium. Tell how violating *any one* of those assumptions would cause the population (gene pool) to evolve and not stay in equilibrium.

* random mating: non-random mating (e.g interbreeding) will cause allele frequencies to change
* no mutations: mutations cause genetic variability → changing allele frequencies
* no natural selection: individuals with greater fitness will reproduce more → allele frequencies change.
* no gene flow: alleles moving from one population into another will affect the allele frequencies
* large population size

violating any of these will result in microevolution!

1-27. Using a specific example, explain the process (sequence of changes) of *evolution by natural selection* for a given trait in a population in a specific environment. 

the british pepper moth: alleles for dark colored moths were rare in the population, but industrial revolution caused dark soot buildup on the tree trunks where moths spend the night; after a few decades nearly all of the moths were dark. 


1. random mutation - the moths had genes for different colors 
2. change in the environment - the trees became covered in soot 
3. individuals with certain traits survived/reproduced more - The dark colored moths reproduce more 
4. change in allele frequency overtime - the moths are now more likely to have alleles for the dark coloring

1-31. Give an example of a genetic mutation (a new allele) that is *neutral* at first (no effect on selection) but could possibly confer a relative fitness advantage in future generations if environmental conditions change. Tell how natural selection could result in an *increased* frequency of a certain allele over time in one environment and a *decrease* in that allele’s frequency when environment changes.

__increased frequency__

* using the pesticide resistance in the mosquito population example, it was neutral with no pesticide, then relative fitness after pesticide was introduced → higher fitness & more offspring. (So there was an adaptive advantage having this resistance gene only after the environment changed)

\n Decreased frequency: Peppered moths, bc of pollution, to survive predators, dark morphs frequency increased. After the Clean Air Act, it greatly reduced the pollution and led to gradual disappearance of environmental soot. The frequency of the dark morph decreased in subsequent years because of this environmental change.

2-4. Distinguish between homology (structures with same ancestry) and analogy (same function).

__homology__

* structure have a common ancestry (divergent)


* Structures may have different functions but share similar underlying structure (e.g. Forelimbs of mammals and birds)  

__analogy__

* structures have similar functions - no shared common ancestry (convergent)
* Evolved independently in different selections due to similar environmental conditions (e.g. Wings of birds and wings of insects)

2-6. Distinguish the three domains of life and the four major groups (”kingdoms”) within the domain Eukarya.

__three domains of life__


1. bacteria: unicellular prokaryotic organisms - no nucleus and DNA is not organized into chromosomes, instead circular loops


1. Peptidoglycan cell wall
2. archaea: unicellular prokaryotic organisms - can survive in extreme environments; various cell membrane components (branched)


1. halophiles, thermophiles, and methanogens 


1. eukarya: have cells with nucleus and membrane-bound organelles

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__eukarya - four kingdoms__


1. protista: Algae and protozoans (mostly unicellular & multicellular)


1. diverse mix of eukaryotic kingdoms, mostly single celled 
2. fungi: mushrooms, yeasts, molds


1. Cell walls w/ chitin 
3. plantae: all plants (mosses, ferns, flowering plants) Multicellular organisms 


1. Apical meristems 
2. (multicellular embryos retained on parent plant)
4. animalia: All animals (jellyfish, mammals and birds), able to move


1. Embryonic germ layers
2. 4 different types of tissue (connective, epithelial, nervous, muscle) 
3. Movement using muscles 
4. Gap junctions,
5. Cell adhesion

2-12. Tell how mitochondria originated by endosymbiosis, and give four types of evidence supporting this.

an ancestor of mitochondria was an aerobic respiration bacteria  that was engulfed into a cell but instead of being digested and broken down it consumed the sugars in the cytoplasm of the cell to carry out aerobic respiration and produced ATP in return creating a symbiotic relationship


1. Double membrane
2. Split by binary fission (asexual reproduction by separation of body)
3. Has its own DNA
4. Circular loop chromosome
5. Both have ribosomes
6. rRNA genes

2-14. Species in many groups have the capacity to reproduce either sexually or asexually. What are the evolutionary advantages and limitations of each, especially related to environmental conditions?

__asexual (__`bacteria`__, archaea, protists)__

* advantages 
* Rapid production growth
* No need for a mate
* Consistency of offspring - identical to the parent - advantageous in stable environments
* limitations
* No genetic diversity - limit the ability of the population to adapt to changing environmental conditions
* Susceptible to environmental changes - affect their survival 

\
__sexual reproduction (plants, animal, fungi)__

* advantages
* Genetic diversity
* Adaptation to changing environments (unique genetic combinations)
* limitations
* Slower population growth
* Utilizes more energy

2-23. For each of these major structural innovations that arose within the history of the Animal Kingdom, tell its function and tell how a group of animals with this structure would have an evolutionary advantage: exoskeleton or endoskeleton, specialized appendages, jaws, amniotic egg

1. exoskeleton: E.g. Arthropods  Harder outer covering provides protection from predators and framework for muscle attachment - movement, keeps water in for insects
2. endoskeleton: E.g. Vertebrates developed hinged jaws for predation
3. specialized appendages: E.g. Wings, legs, arms
4. amniotic egg prevented the eggs from drying out/water leaving but still allows for O2 and CO2 exchange
5. jaws- easier predation

2-24. Be able to use the Boolean operators “AND” and “OR” in setting up a search for references in a search engine like PubMed or Web of Science (from AE4)   \[SKILLS\]

2-29. What are the main functions of the three plant vegetative organs (leaf, stem, root)? Name some special adaptations of these organs in certain plants growing in different environments.

__leaf__: photosynthesis

* floating leaves, waxy cuticle
* photosynthesis is carried out by the fleshy green stems in caci, instead of the spines which are actually the “leaves.”Also use the spines as defense 

__stem__: transportation of nutrients and provides support plant to get sunlight

* Some tendrils are modified stems instead of leaves, like in grapevines 

__root__: absorb water, anchor

* Potatoes have large storage


* Beets store food and water in their roots

2-31. Review __signal transduction__ pathways; tell how when a signal binds to receptor it triggers a cascade of reactions in cell

2-33. Design an experiment to test some specific aspect of plant growth. Formulate a hypothesis and a null hypothesis. Identify independent and dependent variables in the experiment and list control variables that must be held constant for both test and control groups.

### testing if plant grows towards light (phototropism)

* hypothesis: plant will grow towards light
* null: direction of plant growth will not be affected by the light
* controls
* light intensity
* color of light
* dependent: direction of plant growth
* independent: direction of light

3-36. What are plasmodesmata, and how do they function?

* a channel through the cell wall that allows molecules and substances to move back and forth as needed
* connect cytoplasms of adjacent cells by traversing the cell wall

3-38. \[updated\] Distinguish the two factors (solute concentration, turgor pressure) that, together, determine whether the net movement of water (osmosis) will be into the cell or out of the cell.

* water moves towards high concentration of solutes
* water moves away from high turgor pressure

3-39. Describe how proton pumps in root cells help facilitate transport of cations (such as K+ via ion channels), and anions (such as NO3 via co-transport) across plant membranes, and tell how these processes enable water uptake into root cells.

pump H+ out → bring K+ in thru electrical gradient → and NO3- comes in thru cotransport (powered by H+ ions going along their gradient) → water follows those solutes in.

3-41. Explain the upward movement of water in xylem from soil in 
leaves, including the four forces of adhesion, cohesion, root pressure, transpiration. Which force is strongest?

* roots have a lower fluid pressure and higher solute concentration that allows water to go inside the cell → creates an increase in pressure in roots compared to shoot which causes the water to go up along with transpiration also being responsible. 
* transpiration is strongest.
* water evaporates and decreases  water pressure in the area of the leaves. Water will then move towards the area of lower water pressure, causing a cascade of upward movement of water
* adhesion: water clings to cell walls/xylem rather than sliding down
* cohesion: water stick together

2-48.  When a pollen grain nucleus fertilizes an egg nucleus from the same individual plant (self-pollination and self-fertilization), is that the same as asexual reproduction? Why or why not?

* NOT asexual reproduction b/c you’re not making clones
* still meiosis (indp assortment/crossing over) that contributes to genetic diversity
* the surviving megaspore is genetically unique

2-51. Give some examples of flower features that attract different pollinators and how they are related to the sensory system of the animal. What is the evolutionary advantage to a plant of attracting insect visitors that *specialize* on a certain type of flower (color, shape, odor)?

* flowers act as a landing pad for UV insect sight. Odor can mimic mates or other attractive smells to lure unsuspecting insects to disappointment. Specializing on a certain type of flower → that species gets pollinated more (greater reproductive fitness)

2-54. The fruit develops from what flower part? What is the evolved function of fruit?

* Fruit develops from the ovary wall


* The evolved function of fruit: provide nutrition for animals that disperse seeds; an adaptive seed dispersal mechanism that allows animals to disperse seeds

3-1. What is homeostasis? How does negative feedback help maintain homeostasis?

* ability to maintain internal environment within a certain range
* when a variable changes, negative feedback triggers a response that counteracts said change (to bring back to homeostasis)

3-5. Distinguish the general problem in insulin-dependent (type 1) diabetes mellitus from that in non-insulin-dependent (type 2) diabetes.

* type 1: cannot produce insulin b/c pancreatic beta cells are destroyed
* type 2: CAN produce insulin but receptors are not receptive → diet, time meals, exercise

3-6. Tell how the anterior pituitary acts as a master control by secreting tropic hormones. How does the hypothalamus signal the anterior pituitary?

* anterior pituitary secrete tropic hormones which target another gland (ex. thyroid)
* hypothalamus signals pituitary by secreting hormones

3-11. Name the four tissue types and three specialized cell-cell junctions found in animals.

__types of tissues__

* epithelial
* nerve
* muscle
* connective

__cell-cell junctions__

* **tight junctions (selective! blocks interstitial fluid)**
* gap junctions (ion channel)
* desmosomes (loose, linking fibers)

3-14. Name a membrane transport protein, a cell-cell junction, and a cell surface shape (extension) found in transport epithelial cells. Tell how all help maximize specific transport towards the bloodstream.

* lumen → gut epithelial cells → blood
* Na+/glucose co-transporter
* microvilli: increase surface area
* tight junctions: enable specific transport

3-15. How does the Na+-glucose co-transporter help cells take up glucose? What powers that transport?

* **glucose** against its gradient
* **Na+** along its gradient (*generates power for glucose)*

**(Na+/K+ pump** creates *low concentration* within the epithilium cell)

3-20. By what mechanisms do saltwater and freshwater fish maintain their internal osmotic balance?  (different environments, different solutions)

* **saltwater** fish osmoregulation:
* *excretion of salt ions* from gills
* excretion of *concentrated urine*
* **freshwater** fish osmoregulation:
* *uptake of salt ions* by gills
* *excretion of diluted urine*

3-22. In the excretory tubule identify the location of the processes: filtration, reabsorption, and secretion. Distinguish the processes of *filtration* and *reabsorption* in an excretory tubule, as to whether materials are entering tubule or moving into blood.

* filtration: from blood into tubule
* reabsorption: (selective) back into blood from tubule
* secretion: from blood into tubule (H+, Ca++)

3-26. Tell how each of the following would affect the rate of diffusion - increase it? decrease it? not much change? (a) a thicker respiratory epithelium layer; (b) a steeper concentration gradient or greater partial pressure gradient;  (c) an increase in surface area.

a = decrease

b = increase

c= increase

3-36. When plants are attacked by pathogenic microbes, they release a mixture of general anti-microbial substances like hydrogen peroxide. Why might this include a chitin-digesting enzyme called chitinase?

\
* protect against fungi

3-39. List some responses involved in inflammation in the non-specific, innate defense of vertebrates. How do such innate responses protect?

* redness - more blood at surface for defense
* leaky capillaries - white blood cells to attack antibodies
* fever - denatures proteins (antigen)
* swelling - accumulation of fluid to flush things out
* irritation - histamine response
* phagocytes consume foreign substances

3-42. Once a B cell is activated by binding its specific antigen, it clones into many cells, mostly plasma B cells. How do plasma B cells fight free-floating antigen?

\
* secrete antibody proteins which bind to their specific antigen

3-43. How do cytotoxic T (killer T) cells fight their antigen in cells?

\
* target and kill cells infected with their antigen

3-46. How does immunization (vaccination) work?

small dosage of the pathogen leads to mild immune response → memory cells will allow your body to react faster and more efficiently if encountered again

3-47. In neurons, Na+ concentration is much higher outside the membrane, and K+ ion concentration is much higher inside than outside. What helps maintain these membrane ion gradients?

the sodium-potassium pump (pump = ATP!)

3-51. How does specific cell-cell communication happen with neurotransmitters at a chemical synapse?

neurotransmitters are released into synaptic cleft from vesicles found in the presynaptic cleft

V

NT then binds to a receptor

V

neuron transmit signal to post-synaptic cell

3-55. Distinguish how cell-cell communication at chemical synapses between neurons differs from cell-cell communication via gap junctions in cardiac muscle.

* cardiac muscles are connected using gap junctions (no NT’s are being secreted) → ions to move through the membrane → cells to contract synchronously.
* gap junctions: ions pass between cells, can begin depolarization of the neighboring cells
* desmosomes: attachments help couple the contraction of neighboring cardiac muscle cells

4-3. Give examples of three patterns of *dispersion* (clumped, uniform, random). Describe how biotic or abiotic factors may have influenced the pattern.

__clumped__

* social behavior
* effective hunting/caring for babies

__uniform__

* defense of territory

__random__

* random seed dispersal (ex. dandelions)

4-5. (problem) You are studying a population of beetles of size 3000 (N0). During a one-month period, you record 600 births and 300 deaths in this population. Estimate b, d, and r for that first month (What would N1 be?) and project that population’s size (N2) after a second month at the same rates.

4-7. Define "carrying capacity", and name several parameters that help determine it, including both biotic and abiotic factors.

* maximum pop. size that a particular environment can support
* enough food/resources, space (area to grow), remove waste products so they don’t accumulate toxic levels, temperature, competition with others, and type of species

4-8. Distinguish density-independent population controls from density-dependent population controls, give an example of each; and tell how density-dependent factors regulate population growth

__independent__

* natural disasters
* graphed with not reaching K/below and is more random)

__dependent__

* competition for limited resources, disease, predation, competition for nesting space, accumulation of toxic wastes
* stabilizes a population
* there’s a greater rate of loss (graphed with reaching K)

4-10 To understand the relationship between science and society, describe points of view of different stakeholders, for example, on the question of permitting wolf hunting and trapping in lands outside of Yellowstone National Park.

* Farmers were likely pro-wolf hunting/killing since it would benefit them and their livestock.
* Ecologists could be against wolf hunting/killing to protect nature’s natural ways of life.

4-12. Define these general ways in which species interact and give an example of each: predation, parasitism, competition, mutualism, commensalism. Be able to describe how the presence of or increase in one of the interacting species can affect population change in another.

__predation__

* (+)(-)
* increase in predator results in pop. decline of prey

__parasitism__

* (+)(-)
* increase of parasites results in pop. decline of prey

__competition__

* (-)(-)
* increase in one of the species can result in decline of both ?????

__mutualism__

* (+)(+)
* increase in one results in increase of the other

__commensalism__

* (+)(0)
* increase in one has no affect on pop. of the other

4-13. What is the “ecological niche”?  Why is it said that “two species cannot occupy *exactly* the same niche permanently”?

* the sum total of a species’ use of biotic and abiotic resources in its community
* two species cannot occupy the exact same niche b/c there will not be enough resources for both of them (in competition w/ each other)

4-14. Recall the process of evolution by natural selection, and use it to explain how a species could evolve in response to selection as another species interacts with it.

\
* species can naturally to specialize in their niche, resulting in less competition → greater overall reproductive fitness
* Two species using the same resources are competing with each other for this limiting resource and over time if an individual from one species was no longer adapted to eat that particular resource but can still do well in eating something else, there would be a shift. They would no longer compete with the other species because they are doing fine without that old resource. *Competition from the past can evolve a separation.* 

\
Ex: Warblers spread out in different areas of a tree to avoid competition

4-16. Name the major “trophic levels” common to most food chains/webs, and give examples. (how related to community?)

* primary producers
* primary consumers
* secondary consumers
* tertiary consumers
* quaternary consumers
* ex. sunflower → grasshopper → mouse → snake → hawk
* ex. phytoplankton → zooplankton → small fish → bigger fish → orca

4-17. How do foundation species and keystone species have a large impact on biological community structure?

* keystone species: not abundant but exert strong control on the community (ex. otter)
* foundation species: most biomass collectively (spruce, grasses, etc)

4-18. Energy flows through ecosystems beginning with primary producers converting sunlight into chemical energy. Name the major “trophic levels” common to most food chains/webs, and give examples. Why are food chains usually short?

* food chains are usually short b/c biomass is lost in cellular respiration as CO2 and H2O

4-20. Be able to explain: Energy *flows through* ecosystems, and nutrients *cycle within* ecosystems.

* energy flows through ecosystems and exits as heat
* nutrients cycle within with the help of decomposers

4-21. Tell how cellular respiration and photosynthesis *each* individually relate to (a) energy flow and (b) carbon cycling.

__cellular respiration__

* energy flow: lost as heat
* carbon cycling: lost as CO2

__photosynthesis__

* energy flow: energy from sun goes into chemical bonds
* carbon cycling: CO2 from atmosphere into sugars

4-22. Why does total biomass at each level *decrease* when moving to higher levels of the food chain?

* a lot of mass is lost in cellular respiration as CO2 and water

4-23. Explain why there is “biological magnification” of toxins (e.g. DDT, PCBs) as they pass up the food chain, i.e., why substances are higher & higher in concentration in animal tissues

* animals don’t have a way to process contaminants → as organisms get eaten they pass these on to other animals up the food chain

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4-24. Explain the relationship between the increase in atmospheric carbon dioxide (result of human activity) and global temperatures.

* increase in CO2 (greenhouse gas)→ more heat energy trapped and re-radiated in atmosphere

4-26. What is the relationship between changes in atmospheric CO2 levels and ocean pH levels?

* **ocean acidification = aquatic twin of high atmospheric CO2**
* CO2 and water mix and form carbonic acid which dissociates to form H+ and carbonate/biocarbonate → lowers ocean pH


* marine organisms are affected by:
* shellfish unable to make thick, carbonate shells
* hinders growth of coral

4-27. What essential process (reaction) makes atmospheric N2 (abiotic) available for living organisms as NH3?

* nitrogen fixation

4-28. What is “eutrophication”? \[in response to nutrient enrichment\] How do eutrophication events lead to formation of the “dead zone” in the Gulf of Mexico?

* excess of nutrients in water leads to algal blooms → decrease in oxygen → dead zones

4-30. Name three major *threats* to biodiversity today, and give a specific example of each .

* habitat loss: deforestation
* spread of invasive species: imported fire ants
* over-harvesting: over-fishing

4-33. State at least two reasons, one genetic, why small populations are especially in danger of extinction*.[Linking topic, 4/24]*

* lower genetic variability → reduced fitness
* natural disasters are most likely to wipe out the entire pop.