BIOL 112 Final Mega Review PDF

BIOL 112 Test 1: Lyme Disease Origins of Lyme Disease Lyme Disease (LD) was first brought to North America 60,000 years ago by birds ○ NorthEast U.S. now has highest density of LD in the world Lyme, Connecticut (1970s): large outbreak of target ‘bulls-eye rash’ lesions affects...

BIOL 112 Test 1: Lyme Disease Origins of Lyme Disease Lyme Disease (LD) was first brought to North America 60,000 years ago by birds ○ NorthEast U.S. now has highest density of LD in the world Lyme, Connecticut (1970s): large outbreak of target ‘bulls-eye rash’ lesions affects population, allowing for the identification of LD (and the bacteria that causes it by Dr. Willy Burgdorfer) ○ *Quiz question: One of the difficulties in diagnosing LD is* The long length of time between the tick bite and the onset of symptoms Borrelia burgdorferi: bacteria whose effect (LD) is specific to NE U.S. Black-legged ‘deer’ tick: (Ixodes scapularis): carries Borrelia ○ *Quiz question: How long does LD infection require a tick feed on a host for?* At least 24 hours White-footed ‘deer’ mouse: the main host for LD that acts as a reservoir for Borrelia bacteria Tick and Lyme Disease Transmission Lifecycle *Learning objective: define vector and host, identifying them in the transmission of LD* Vector: organism that transmits the pathogen Host: an organism in which the pathogen is from one host to another living Ticks— Hosts differ in competence: the ability to catch a pathogen and pass it on to another White-footed mice—highly competent: 80% of the time when an infected tick feeds on a mouse, the mouse will infect a second tick too! Robins (small birds that forage for food on the ground) Mammals— Humans—are a dead-end due to low competence Incompetence is due to our immune system and the fact we are new to Borrelia Ticks are not born with Borrelia; they have to feed on an infected host in order to obtain it 1  ○ As ticks feed on more hosts, they may contract more strains of Borrelia (and other pathogens, causing coinfections) Ticks have 4 life stages (eggs, larva, nymph, adult): in order to progress from one stage to the other, they must feed first; ticks feed only once each stage ○ So, humans can’t get infected with Borrelia by larva, because then we would be the first host, and the larva doesn’t have Borrelia yet ○ To keep the cycle going, larval AND nymphal ticks must feed on mice: first to be infected, then to infect! Year Season Life Stage Host(s) 1 Spring Eggs None 1 Summer Larva Small-bodied animals (first feed): Robins (and other small songbirds) White-footed mice Larva will latch 2  for a couple days for blood, it not too long so they aren’t killed 1 Fall Larva *metamorphosis* 1 Winter Larva *metamorphosis* Larvae will overwinter in leaf litter 2 Spring Nymph Large animals (second feed): Nymphs look for larger animals— so their now-larger body size will be less-likely to be noticed 2 Summer Nymph *metamorphosis* Risk of Stage most likely to human spread LD to humans: infection is ○ Small enough greatest in late to go unnoticed spring and ○ Spring/summer summer! less clothed and more extended outside activity ○ Actively looking for larger animals like humans 2 Fall Adults: Even larger animals Less of a threat to humans: ○ Larger body easier to notice ○ Wearing more covered clothes 3  ○ Less outside activity STILL, MORE DEER —> MORE HOSTS FOR ADULT TICKS —> MORE TICKS —> MORE HUMAN INFECTION 2 Winter Adult Mate, reproduce, then die Ecosystem and Lyme Disease *Learning objective: define organism, population, community, and biosphere, applying them to the tick/LD system* 1. Organism: single individual 2. Population: a group of interbreeding organisms that are members of the same species living in the same area are the same time a. Conspecifics: Organisms that are all members of the same species 3. Community: Consists of all the different species within an area a. Heterospecifics: members of different species 4. Ecosystem: composed of all the living (biotic) and nonliving (abiotic) things of the area 5. Biosphere: Encompasses all of the ecosystems on Earth *Learning objective: What are the characteristics of all living things?* 1. Made up of cells 2. Metabolism: convert molecules from the environment to new biological molecules 3. Contain genetic material 4. Reproduce 5. Populations evolve overtime Biotic: living components of the environment Abiotic: non living components of the environment Population of black-legged ticks Temperature: ticks more active in Population of white-footed mice warmth Tree leaves on ground (foraging site) Humidity: ticks thrive in moisture ○ Gives ticks an area to lay eggs ○ Ticks are vulnerable to dying and overwinter (as well as out nymph overwintering) Pesticides ○ Provides moisture and High elevations: more fog and protection humidity Human activity/ behavior Biogeography: the study of the ○ Clothing geographic distribution of living 4  ○ Trails things and the abiotic factors that Amount of predators (birds, pets, affect their distribution foxes, snakes) Net primary productivity: an Forest condition (fragmentation) estimation of all the organic matter ○ Smaller patch size —> less available as food biodiversity —> fewer ○ Measures as above-ground predators and abundance of biomass: total mass of living mice plants *Quiz question: Every disease that involves a pathogen has an ecology: abiotic and biotic factors affect its spread and distribution. The ecology of LD involves:* Multiple pathogens that often spread at the same time as the LD bacteria Mast year: a year when oak trees make A LOT of acorns ○ Correlated with the average temperature (abiotic) in May: warmer spring indicates bigger mast year 5  ○ More acorn food means a huge increase in mice population—mice grow quickly because they reproduce at 1 month old ○ Tick population increases too because of the increase of hosts it can find the FOLLOWING (next) spring ○ Borrelia spread A LOT, increasing inflections of LD (the next year) Zoonoses: pathogen-caused disease that moves between humans and non humans (viral or bacterial) ○ Ex) malaria, Zika, rabies, bubonic plague, swine flu, COVID (in deer/rats), LD (Re)emerging diseases: diseases of rapidly increasing incidence (that were previously under control) ○ Ex) tuberculosis, Climate Change and Lyme Disease *Learning objective: distinguish between climate and weather* Climate Weather Long-term pattern: years, decades… Short-term pattern: can occur in a day (usually made in 48 hour cycles) *Learning objective: Define biome and give examples* Biome: an area of Earth with similar/same climate (precipitation patterns, temperature, humidity) and species (flora + fauna) within ○ Ex) the desert is dry (low humidity + low precipitation), has high insolation (sun exposure), and is home to many reptiles (snakes, lizards) *Learning objective: Identify which biome an organism most likely lives in* 6 *Learning objective: Apply the concept of biomes to different systems (humans, ticks/LD)* Terrestrial biomes: rainforest, temperate deciduous climates, season length *Learning objective: Explain and create hypotheses for the spread of LD* *Quiz question: How is our warming climate affecting Ixodes ticks in North America?* 7  1. Ticks are spreading into areas that were previously too cold for them 2. Ticks are becoming more common in places they used to be rare LD is spreading NorthEast Nymphal ticks are emerging earlier in the spring Warmer winters accelerate ticks lifecycles and allow them to survive further north each year HOWEVER, INCREASED SUMMER TEMPERATURES (UNACCOMPANIED BY MOISTURE) LOWER TICK SURVIVORSHIP Increased greenhouse gases —> increased humidity —> ticks survive longer ○ In the South, there is less rain and humidity —> reducing tick activity *Question: Why are there areas with a high population of Ixodes presence but low cases of LD* There is a difference on what the Ixodes ticks are feeding on ○ NorthEast: ticks feed on mice, which are highly competent ○ Southeast/West: ticks feed on lizards (which are highly incompetent. This is caused by biotic factors (species of lizard is not found in the NorthEast) and abiotic factors (the NorthEast climate/cold is nor suitable for the lizard) *Learning objective: Define the greenhouse effect and global climate change* Greenhouse effect: warming of Earth due to carbon dioxide and other greenhouse gases in the atmosphere (that absorb and emit radiation, thus trapping heat) ○ *Learning objective: list two greenhouse gasses, describe how they’re released into the atmosphere, and describe their role in the greenhouse effect* ○ Nitrous oxide: fertilizers in farming, fossil fuel combustion ○ Methane: cow flatulence in feedlots, landfill decay 8 *Learning objective: summarize the effects of the Industrial Revolution on global atmospheric carbon dioxide concentration* Global climate change: altered global weather patterns, including a worldwide increase in temperature, due largely to rising levels of atmospheric carbon dioxide *Learning objective: Discuss evidence of global climate change; Identify patterns observed in data and made predictions on data* 9  CO2 concentration is cyclical overtime with DRASTIC fluctuations Large temperature anomalies: 1. Medieval Warm Period: 2. Little Ice Age 3. Industrial Era Humans are about 200,000 years old, meaning that the CO2 peaks existed before us *Quiz question: Before human-caused changes, this main drivers of global climate change have been—* 1. Milankovitch cycles: cyclic changes in the Earth’s orbit that affect climate 2. Variation in the sun’s intensity 3. Volcanic eruptions a. Haze-effect cooling: dust, ash, or any other suspended particles block our sunlight and trigger lower global temperatures as a result Patterns of temperature change and CO2 concentration appear to match: strong correlation ○ Due to the greenhouse effect, etc. ○ They can drive each other 10  The Keeling Curve: plots the ongoing change in concentration of CO2 Samples were taken from Mauna Loa, Hawaii: which is not industrial nor near land so, it contains a very pure/uncontaminated measure of atmospheric CO2 in Earth’s atmosphere Curve shows overall increase in CO2 BUT annual variation based on seasonal cycle ○ Spring/Summer: plants photosynthesize and take-in the CO2 (at a greater rate than respiration occurs) ○ Fall/Winter: plants decompose, releasing CO2 with increased respiration rates (which isn’t being taken in anymore because photosynthesis has slowed) ○ *Question: Then why wouldn’t the levels be balanced, since seasons are reversed in the Southern Hemisphere?* ○ There is more land in the Northern Hemisphere than the Southern Hemisphere, so the Northern plants dominate 11  Drilling for ice cores in the polar regions: the ice contains air bubbles (that contain gas in the atmosphere from thousands of years ago that scientists analyzes for CO2 concentration) and biological substances/debris (such as pollen and bacteria) *Learning objective: Describe impacts of climate change* Displacement of polar bears, forcing them to move southward Increased forest fires (due to drying out) Increased risk of spread of infectious disease (warmer temperatures allow vectors to survive/thrive in area they couldn’t before) Ocean acidification Number of heat related deaths has increased Retreat of Grinnel Glacier: melt water runs down mountainside to supply people with water Melting of clathrates: frozen chunks of ice and methane at the bottom of the ocean ○ Positive feedback loop: warm water causes, ice melts and causes methane to be released…. Phenology: the study of the effects of climatic conditions on the timing of periodic life cycle events ○ Ex) flowering in plants, pollination, migration in birds, hatching of nymphs 12 Population Ecology and Lyme Disease *Learning objective: Define density and apply it to biotic systems* Population density: the number of individuals within a specific area or volume ○ Populations with higher density may be more stable based on their genetic variability, and thus their potential to adapt to the environment ○ Populations with lower densities are more spread out in the habitat, and may have more difficulty finding a mate to reproduce Population density typically decreases with increasing body size Smaller organisms tend to be more densely distributed than larger organisms *Learning objective: Discuss resource limitation; predict the impact of changes in resource levels on populations and communities* Resource limitation: limitation of population growth by resource availability *Learning objective: Describe and list population distribution patterns* 13  1. Uniform: a. Ex) Penguins space out evenly because they are very territorial (maintain a defined territory) b. *Quiz question: One reason that plant individuals of the same species might occur in uniform distribution is that they* Release allelopathic (inhibit growth) chemicals into the soil around them 2. Random: a. Ex) Dandelions are spaced out randomly because wind gusts blow their seeds in random locations b. Solitary species within a random distribution may have difficult finding a mate 3. Clumped: a. Ex) Elephants are clumped together because they are social beings that engage in herd behavior b. *Test question: How would clumping be in oak trees during Mast year?* They would be clumped in a mast year, and spread out other years *Learning objective: Understand age structure and survivorship* Life Table: Used to depict the life expectancy (how many more years expected to live) of a population member based on its age ○ Uses a cohort of individuals starting at birth Mortality rate: proportion of population surviving at the beginning of an age interval that die during the age interval— (number of individuals dying / number of individuals surviving) x 1000 14  Survivorship of a species varies across time and space—*be able to explain these factors* *Learning objective: Describe the three survivorship curves and explain the life histories of organisms that exemplify each curve* 15  Type 1: high percentage of offspring survive their early and middle years— death occurs mostly in older individuals ○ Have high survivorship in youth ○ Produce small amount of offspring ○ Use A LOT of parental care ○ Have longest lifespan ○ Ex) humans (mammals), crocodiles/alligators, deer Type 2: die more or less equally at each age interval ○ Consistent rate of dying/surviving throughout life ○ Provides parental care ○ Once a resource depletes, the move onto another ○ Ex) birds (robins, cardinals) Type 3: very few individuals surge their younger years; but those that make it to an old age are more likely to survive for a relatively long period of time ○ Have high die-off when young ○ Those who survive live longer ○ Little to no parental care ○ Ex) insects, sea turtles ○ White-footed mice: though usually like Type 3, during Mast years the babies would survive more and therefore exhibit Type 1 survivorship * Learning:objective Link survivorships curves to concepts of r- and K-selection* r-selected: increase exponentially ○ Often connected to Type 3 survivorship K-selected: live under equilibrium conditions ○ Often connected to Type 1 survivorship 16 *Learning objective: Understand growth curves and interpret them to describe what is happening in a population* Exponential Growth curve: dN/dt = rN dN/dt: instantaneous growth rate describing a change in population size (N) r: intrinsic (species) rate of increase = birth rate - death rate ○ Growth rate (r) doesn’t change even if population (N) gets very large; any chance is due to higher population of moms having children ○ If r is positive, the population is increasing ○ If r is negative, the population is decreasing ○ If r is 0, the population isn't changing ○ If r is large, the population grows rapidly and the curve is steeper ○ If r is small, the population grows slower and the curve is flatter rmax: growth rate under ideal conditions (biotic potential) Exponential growth can only occur when a population has access to unlimited resources (ideal conditions); occurs only in short-term conditions ○ Ex) virus in body, new invasive species (spotted lantern fly) Darwin’s Elephants: Elephants have children when they’re older and usually have 1 child at a time (with long pregnancies), resulting in a small r of 0.01 ○ Fecundity: potential reproductive capacity of an individual ○ Selection keeps numbers low so exponential growth doesn’t apply all the time ○ Deer: r = 0.5 ○ Mice: r = 16 Logistic Growth curve: dN/dt = rmaxN((K-N)/K) Growth rate r changes and gets smaller as approaches K K: Carrying capacity, the maximum population size that resources in the environment can sustain 17  ○ If K=N: dN/dt would be 0 and population would be constant ○ If K < N: dN/dt is negative and population decreases ○ If K > N: dN/dt is positive and population increases *Test question: Know how to manipulate parts of formulas* Intraspecific competition: *Quiz question: Intraspecific competition plays an important role in populations that grow logistically, because intraspecific competition:* 1. Is initially weaker than interspecific competition, but this changes at K (doesn’t affect populations that are well under their carrying capacity— there is an abundance of resources for everyone) 2. Causes the population growth rate to decrease as the population grows 3. Can play an important role in determining carrying capacity (including accumulation of waste products) 4. Is the result of phenotypic variation in members of the population (some will be better adapted to environment than others) 18 *Learning objective: Connect r- and K- selection to survivorships curve, growth curve, and density-independent/dependent factors* Density-independent: factors that affect population size (N) but are not initiated by the population ○ Ex) forest fires affect tick numbers, rainfall, etc. ○ Tend to be abiotic Density-dependent: factors that affect population size (N) that originate from the population ○ Ex) predator-prey relationship, competition, disease, etc. ○ Tend to be biotic ○ The denser the population, the greater its mortality rate (during intra- and interspecific competition, reproductive rates of individuals will usually be lower, reducing the population’s rate of growth) r-selected: Specialized in maximizing their ‘r’ K-selected: spend most of their time at ‘K’ growth rate by finding/exploiting resources carrying capacity; conditions stay the same and reproducing in unpredictable/changing (stable and predictable)—individuals must be environment— K has no meaning good in them (be able to compete within species) Mice— Deer— r-species: grow fast and use resources K-species: few offspring (especially during Mast year) ○ Body size: large (requires ○ Body size: small (requires less longer gestation and therefore materials to make, so slower reproduction) reproduction is faster) —> ○ Population density: lower high r-values ○ Survivorship: Type 1 ○ Population density: HIGH More impacted by density dependent DENSITY factors ○ Survivorship: Type 3 ○ Live most of life at high More likely to be impacted by density density-independent factors Growth: logistic ○ Usually scattered ○ NOT LIMITED BY K IMPACTED LARGELY BY ABIOTIC FACTORS ○ indicated by lack of K Growth: exponential *Test question:* 19  Observation: As spring temperature increases, acorn production increases Do you have any concerns regarding this figure? ○ Correlations doesn’t equal causation; a confounding variable could exist ○ Large error bars ○ If the rightmost data point was removed, the trendline would be VERY different Are the causes of the fluctuations in mouse populations abiotic or biotic? ○ Both (?) ○ Biotic: Oak trees produce a large amount of acorns during Mast year ○ Abiotic (better answer): Seasonal effects— Spring temperatures drives increased production of acorns 20  Are the rabbits r- or K-species? ○ r-species: No appearance of ‘K’ carrying capacity; appears to have high ‘r’ *Test question: What impacts rabbit growth? Biotic or abiotic?* ○ Answer: BOTH Biotic: Abiotic: Viral disease: High food resources Rabbits develop/evolve better Natural events (drought) immune responses AND Pathogen evolves to become less lethal (to decrease chance of killing host, and increasing chance of being transferred) ○ Ex) COVID 21 *Question: Growth rate has skyrocketed, why?* Healthcare/modern medicine Having more children *Question: Growth rate is crashing, why?* Having babies later in life Have less babies/ no babies at all Even though we have the highest calories consumption in history, new medical technology, and highest infant survival rate yet— our population is (and will continue) declining ○ We are the only species to improve conditions by reducing reproduction ○ We aren’t following exponential OR logistic (in the future?)! Neither curve suggests that population size will decrease! Community Ecology and Lyme Disease 22  Lynx population lags 1-2 years behind the hare population (because the hares reproduce faster) The lynx population controls the hare population, and the hare population contributes to the lynx population ○ We can predict the future (about 2 years?) lynx population based on where the hare population is Cycling in hare can also be caused by density-dependent effects: crowding causes lower fecundity (maternal stress) *Question: are all prey populations controlled by their predators?* NO: not all prey populations are determined by the predators ○ Species who are usually impacted by density-independent factors AND/OR whose reproduction is controlled by abiotic factors ○ Ex) Mosquito population depends on access to water/ whether it’s a wet year Predators can induce physiological stress responses in their prey *Learning objective: Adaptations against predation and herbivory:* Mechanical defenses: discourage predation/herbivory by causing physical pain or physically prevention ○ Ex) thorns in plants, hard shell on turtles Chemical defenses: ○ Ex) toxic when eaten Camouflage: avoiding detection by blending in with background Aposematic coloration: warning coloration for foul taste, toxic chemicals, or stinging ○ Predators who experience this learn not to eat these organisms in the future Batesian mimicry: a non-harmful species takes on the warning coloration/appearance of a harmful species Müllerian mimicry: species share warning coloration/appearance and are all harmful to predators 23  ○ *Quiz question: The viceroy butterfly and the monarch butterfly are similar-looking and well-known North American butterflies that are distasteful and even toxic to predators. This is an example of:* Müllerian mimicry Emsleyan/Mertensian mimicry: a harmful species resembles a less harmful species Plant-herbivore: Species diversity: number of species occupying the same habitats and their relative abundance ○ Species richness: number of different species in a community ○ Relative species abundance: absolute population size of a particular species relative to the population sizes of other species within the community Competitive Exclusion Principle: no two species within a habitat can coexist when they compete for the same resources at the same place and time Symbiosis: close interaction between individuals of different species over an extended period of time that impacts the abundance and distribution of the associating populations *Quiz question: Biogeography determines which species are found on Earth, and Borrelia is only found where ticks of the genus Ixodes are found. Ixodes ticks, however, occur in many places without Borrelia. This suggests their relationship is:* Symbiotic Commensalism: One species benefits, while Bird nests in trees the other is unaffected Ticks in long/high grass Borrelia in ticks and mice Mutualism: Both species benefit from the Birds dispersing plant seeds relationship Moving pollen 24  Algae and fungus Humans and bacteria in digestive track Parasitism: One species benefits, while the Ticks on hosts (mice, deer, humans, other is harmed etc.) **Question: How does the invasive Japanese barberry bush affect LD?** Invasive species: introduced species that harms its environment due to lack of natural predators/competitors Barberry has taken over the Long Island understory by outcompeting and replacing the native grass ○ Holds moisture really well, which is a great environment for ticks to hide and thrive (+) Deer often eat native plants, but can’t digest barberry ○ *Test question:* Since deers are important hosts for adult ticks, so if they migrate, it may harm the tick population (-) Small birds are important hosts for nymphal ticks; when they migrate or fly, they bring the ticks with them long distances ○ Symbiosis: The barberry has fruits; when the birds eat the fruit the drop them around, growing the barberry population and territory *Learning objective: Explain how abundance/removal of a one species affects the others in the community* Keystone species: species whose presence is key to maintaining biodiversity in an ecosystem and to upholding an ecological community’s structure Where there are foxes there is less LD ○ Foxes are specialists at hunting mice—they can control the mice population at a high enough density Places with more coyotes per fox have more cases of LD 25  ○ Coyotes introduced to the East coast outcompete (and sometimes predate on) the foxes —> coyotes displace foxes, so more mice survive —> more mice carry more Borrelia for more LD ○ Habitat disruption also impacts fox populations because they need large patch sizes Homeostasis and Temperature Stress Homeostasis: A narrow range of stable physical and biochemical conditions under which the body functions optimally (dynamic equilibrium) ○ Active maintenance of internal conditions that are relatively stable and different from external conditions ○ Necessary for survival: adapt to new environments and maintain health Set point: midpoint or target point in homeostasis (can change regularly) ○ The body raises its temperature set point at the beginning of a fever and lowers it when the fever breaks Acclimatization: adjustment in a body system in response to environmental change ○ Changes/responses made in a group of body organ systems in order to maintain set point in another system ○ *Quiz question: Each winter, Long Islanders adjust to the cold weather by raising our BMR, and doing the reverse in the summer. This is similar to deer and mice growing thicker fur in the winter and thinner fur in the summer. These are examples of:* Acclimatization Negative feedback loop: feedback to a control mechanism that increases or decreases a stimulus instead of maintaining it ○ Whenever there’s a deviation from the preferred set point, the body brings it back (and process stops when set point is reached) *Question: When do we change our set point for temperature?* ○ Sleep (cools down) 26  ○ Seasons (winter vs summer) ○ Fever (temperature raised then brought down) *Test question: Identify each part of the feedback system* Stimulus: the change in the environment Receptor: the sensor that detect the change (in a variable) Input: the information/signal sent to the the control center from the receptor 27  Afferent pathway: the direction the information moves towards the control center Control center: monitors and reacts to deviations from the set point (?) Output: the information/signal sent from control center to the effector Efferent pathway: the direction the information moves from the control center Effector: the component that causes the change Response: changes/returns variable Positive feedback: feedback or a control mechanism that continues the direction of a stimulus ○ Response of the effector feeds back to INCREASE the effect of the stimulus ○ Very rare; getting further and further from optimal conditions Feedforward information: Body prepares to change set point in advance ○ Very common feature of negative feedback loops ○ Alteration: change of the set point in a homeostatic system feedback loop ○ Body finds regularity/patterns in our behavior and adjusts so (ex: sleeping schedules) ○ Body adjusts in advance to future needs, even though stimulus isn’t there yet (ex: minutes before starting a race, sets heartbeat higher) *Question: How do organisms deal with temperature stress?* Thermoregulation: the processes of homeostasis and temperature control are centered in the hypothalamus of the advanced animal braim 1. Start here: set point set at 98.6 F 2. Input/stimulus detected by sensors 3. Sensors send information to regulatory system 28  4. Compare input/stimulus to set point 5. If not equal, error signal sent 6. Control systems receive error signal 7. Control systems initiate response 8. Deviation from set point decreases 9. Set point achieved *Learning objective: Describe physiological and behavioral tactics used by organisms to maintain temperature homeostasis* Tolerate temperature change Lose excess heat if hot Minimize heat loss if cold Gain heat from internal/external source Hibernate or become dormant ○ Torpor: decrease in activity and metabolism that allows an animal do survive adverse conditions ○ Estivation: allows animals to survive hot, dry climate Move or migrate ○ But carries risk and comes at high-energy cost Humans must conserve heat, because staying warm is energetically expensive *Question: So how do we stay so much warmer than the air around us?* 29  We have internal processes to produce heat; cellular respiration breaks down/burns blood sugar to produce ATP and heat as waste ○ We have to consume A LOT of calories to keep warm Surface area-to-volume ratio (SA:V): ○ When SA:V decreases, diffusion becomes less efficient ○ * Quiz question: SA:V issue affect everything in our bodies (from how our lungs are structured to the changes in calories needed as we grow from infancy to adulthood). Which of these SA:V statements is correct?* As a baby, you had a greater surface area for your mass than you do now *Question: How do elephants stay cool?* Because elephants are so big, they have little surface area compared to volume (SA:V), so they have difficulty getting rid of heat ○ Live in warm places as warm-blooded animals ○ Can’t run for long or exert themselves without overheating Methods— Spray self with water, stay in shade, fan self with ears Their ears are very vascular (contain many veins/arteries), so they will send more blood to their ears to cool the rest of their bodies *Question: how do penguins stay warm?* Baby penguins are small (high SA:V) so they have issues retaining heat Methods— ○ Huddle together ○ Special hair-like feathers that act as insulators ○ Walk on parents feet to not lose heat to condition with ice ○ Vasoconstriction: reduces blood flow to peripheral blood vessels, forcing blood to the cure and the vital organs there, conserving heat (ex: Keep feet cold in general to warm rest of body) POPULATION EVOLVES BODY TRAIT —> INCREASE OR REDUCE SA/V —> MAXIMIZE OR MINIMIZE HEAT LOSS *Learning objective: How do ticks survive the winter?* Go into low-energy state (torpor) for a few seats, and resume searching for blood after Survive low temperatures by drawing water out of cells before it crystallized Ticks feed on warm-blooded creatures, so lets them be active in the cold ○ If a larva or nymph hasn’t fed yet, they will stay inactive until temperature rises Reduced snow cover allows them to survive and nest in leaf litter Plant adaptations to the cold: Problems— Solutions— 30  Variable water availability Deep root systems Variable humidity Annuals (r-selected): rapid growth and Variable temperature reproduction Variable light Thick bark (K-selected) Rolled/needles leaves with waxy coating Drop leaves (deciduous) to reduce water loss Antifreeze sap/resin prevents cells from bursting when frozen *Learning objective: How is heat exchanged?* Radiation: the emission of heat waves from the sun Evaporation: heat is removed with liquid from a surface (ex: sweat) Convection: currents of air remove heat from the surface of dry skin as the air passes over it Conduction: Heat will be moved from one surface to another during direct contact (ex: animal laying on rock) Endotherm: animal capable of maintaining a relatively constant internal body temperature ○ Generate heat through metabolism (cellular respiration); use that heat to maintain high body temperatures ○ Thermogenesis— brown fat cells have many mitochondria and produce heat Ectotherm: animal incapable of maintaining a relatively constant internal body temperature ○ Don’t use metabolism constantly ○ Have difficulty changing their internal temperature from that of the environment ○ Adjust physiology or location Poikilotherms: animals with constantly varying internal temperatures Homeotherms: animal that a contestant body temperature in the face of environmental changes 31  Basal metabolic rate (BMR): metabolic rate at rest or fasting (?) in endothermic animals Standard metabolic rate (SMR): metabolic rate at rest in ectothermic animals ○ In the cold, the lizard (ectotherm) has a very inactive metabolism ○ In the warmth, the lizard (ectotherm) has a much higher metabolic rate Thermoneutral zone: ○ Temperature of the environment matches the internal temperature of the organism ○ Endotherm uses very little energy and is most comfortable Topics in textbook/reading that are not at all mentioned in class: EMAIL Animal form/body planes Conditioning Succession Poikilotherms and homeotherms: what is the difference between a homeotherm and an Endotherm? a Poikilotherm and an ectotherm? SAME THING Spring-and-fall turnover and thermocline What is the difference between acclimatization and alteration? ○ Alteration: more to do with set point ○ Acclimatization: more do with response of body system Triangle???? 32  BIOL 112 Test 2: Isle Royale Intro to Isle Royale Isle Royale is a remote island in the Great Lakes Formed by glaciers Island first exposed 10,000 years ago ○ Fir trees arrived around the same time ○ Humans arrived 5,000 years ago (well adapted to cool conditions) ○ Moose arrived more recently (around early 1900s) and came by swimming ○ Wolves arrived in the late 1940s and came by ice bridge Ice bridges were once common, but now form rarely (and irregularly) now due to climate change Energy and Trophic Levels Food chain: ○ Grazing: has plants or other photosynthetic organism at its base ○ Detrital: has organism that feed on decaying matter (decomposers) at its base *Quiz question: Ecosystems are among the most complex systems available for direct study by biologists, far more complex than a single human body. One problem with the food web approach to studying ecosystems is that—* Food webs are often not completely linear, because some species may feed on prey from more than one other level Trophic pyramid: ○ Primary producer: photosynthetic organisms at the bottom of the food chain ○ Primary consumer: the organisms that consume the primary producers ○ Secondary consumer: the carnivores that eat the primary consumers ○ Tertiary consumer: the carnivores that eat other carnivores ○ Apex predator: the organisms at the top of the food chain Trophic cascade: *Question: Why do some trophic pyramids have many levels, and others have fewer? What determines how many levels there are?*  Using the POV of energy… ○ After a limited number of trophic energy transfers, the amount of energy remaining may not be large enough to support viable populations at a higher trophic level ○ Energy flow: Primary Productivity Hypothesis (“Bottom-up”): ○ Who are the primary producers? Patterns driven by plant abundance ○ The number of levels AND the number of individuals in each level is determined by how much energy comes in at the bottom (sunlight) ○ If what’s at the bottom is increased, then everything above it will increase too Sunlight, water, length of growing season ○ Ecosystems are structured/controlled by how plants fix energy into glucose Trophic Cascade Hypothesis (“Top-down”) ○ Patterns driven by level directly above ○ Wolves control moose, and the moose control fir trees in turn ○ During the time that moose were present in Isle Royale and the wolves were NOT, moose could reproduce w/o any predators controlling their numbers ○ When wolves first arrived, they reduced the moose population a lot, which increased the fir tree population *Quiz question: If the wolf-moose-fir tree ecosystem on Isle Royale is a bottom-up controlled ecosystem, what relationship would we expect if we looked at a graphical plot of wolf densities vs. moose densities (assuming that wolf abundance is primarily determined by food availability and moose abundance is primarily determined by food availability)?* Wolf and moose abundances would be positively correlated Wolf/Moose Dynamics Resistance: ability of an ecosystem to remain in equilibrium in spite of disturbance Resilience: the speed at which an ecosystem recovers equilibrium after being disturbed *Question: What would your prediction be in terms of tree abundance when wolves are removed?*  Trophic cascade hypothesis: tree abundance decreases— less wolves mean more moose and increased herbivory on trees Primary productivity hypothesis: no change— control doesn’t come from the top; wolf population wouldn’t have an effect (bc the wolves don’t kill enough moose, they just reproduce and bounce back) Answer: both, depending on time period *Quiz question: Actual Evapotranspiration (AET) is important here because we can use it—* as a measure of Net Primary Productivity *Learning objective: Draw a biomass pyramid for the wolf, moose, fir tree system* Can assume these species are K-selected; can expect primarily biotic and density-dependent factors, but sometimes BOTH The highest level supports the smallest biomass *Quiz question:* Wolf pack behavior— ○ Wolves get less food in packs; they kill moose more frequently, but have more mouths to feed ○ Wolves are followed by ravens who wait to eat leftovers from wolf kills; this is why wolves live in packs! to avoid losing too much food to ravens Biotic factors for dynamics—  ○ Tick populations Moose can get infected with LD when tick populations are dense (during summers after warm winters) Ticks cause major irritation in moose (scratch off fur, don’t eat much, distracted from predators) ○ Brain-worm parasite Are considered natural (unlike Parvovirus 1981 in wolves) Passed by deer when the deer population is high Makes moose more vulnerable to predation Abiotic factors for dynamics— ○ Winters Brutally cold Deep snow makes it difficult for moose to find plants, causes moose to get stuck/sink in snow Kills ticks so they won’t be as large of a problem next year Forms ice bridges to allow new wolves to arrive ○ Summers Dryness reduces graze material for moose Adaptations: a trait (structural/physiological/behavioral) that increases an individual’s chance of survival and reproduction in its environment ○ Ex) speed/canines for wolf, ability to run-away for moose, and unpalatable chemicals for plants Plant adaptations— ○ Why do plants need water? To perform photosynthesis, transpiration, and to stay upright (avoid wilting) ○ Where do they get their water? Soil, location in freshwater, and turning saltwater into freshwater ○ How do they lose water? Evaporation and transpiration Photosynthesis and Cellular Respiration Why is photosynthesis so important? ○ It is a method of storing chemical energy from solar radiation to energy in the carbon-carbon bonds of carbohydrate molecules (*Quiz question:* which can be passed to other organisms) Plant and animals cells— Similarities Differences Nucleus Plant cell wall Mitochondria Plant large vacuole ER Plant chloroplast  … Mesophyll: the leaf’s middle layer where photosynthesis occurs *Quiz question: Which of these answers correctly starts with the most inclusive and becomes gradually less inclusive?* Leaf, mesophyll, chloroplast, granum, thylakoid, chlorophyll, thylakoid lumen  *Quiz question: The complete list of all photoautotrophs includes—* 1. All plants 2. All algae 3. All cyanobacteria Part 1: Light Dependent Reactions 1. Light energy strikes leaf —> cell —> chloroplast —> receptor molecules. When hit, the receptor molecules release an electron 2. The electron gets passed between molecules via a chain  3. Water from lumen gets split into oxygen and hydrogen (the first products) 4. Floating protons build up in lumen 5. Electron hooks a proton to NADP to form NADPH (a high energy molecule to do work/store energy) 6. Protons help convert ADP and phosphorus to form ATP (another high energy molecule) Part 2: Light Independent Reactions 1. In the stroma, 2ATP, NADP, and CO2 (dissolved in stroma) are used to form glucose Keeling Curve— ○ New CO2 levels emerging due to glucose that was fixed in the past (carbon molecules from hundreds of millions of years ago) Burning them = releasing the ancient carbons now ○ Seasonal variation: explained by photosynthesis cycles (humans not as responsible for annual up-and-downs of CO2) *Know the role of water in photosynthesis* Water is needed for the Light Dependent Rxns to occur ○ So plants don’t need water at night bc they can’t do light-dependent rxns in the dark anyway Most plants use their roots to get water Epiphytes: obtain water from rain (grow in humid climates and can store water: *Question: How does the plant get CO2?* Stomata: ○ Lets gasses in and out (when closed, gasses can’t move in and out) ○ Also important for water vapor—open stomatas means that water is being lost to evaporation Guard cells: control opening and closing based on turgor pressure *Test question: What happens in a plant that experiences water stress?* 1. Stomates closed/closing 2. Light-independent rxns stop (no new CO2 is entering, and all remaining CO2 is used to make sugar) 3. Light-dependent rxns stop (due to lack of water) Timing of light-dependent vs light-independent rxns stopping depends on CO2 vs H2O availability. They’re at competition— ○ Stomates closed: save water, less CO2 ○ Stomates open: more CO2, less water vapor *Question: How does the plant release the O2 it produces?* Oxygen isn’t needed for photosynthesis, but for cellular respiration Plants do less cellular respiration (and thus require less oxygen) bc they’re less metabolically-demanding (inactive) ○ so plants have excess oxygen—released as waste product! Carbon and Oxygen cycles in the Anthropocene (current time) ○ Carbon cycle: ○ Oxygen cycle:  Endosymbiotic theory: Mitochondria and Chloroplasts… ○ Have their own double membranes (like the nucleus and cell wall) ○ Have their own DNA they divide like cells (mitosis)  similar to that of bacteria ○ Reproduce like bacteria Hypothesis: chloroplasts and mitochondria were once their own bacteria Mutualism w ancestor cells Cells w removed mitochondria can’t create replacement mitochondria *Quiz question: One difference between autotrophs and heterotrophs is—* Autotrophs need carbon dioxide to make carbohydrates and heterotrophs need oxygen to break down carbohydrates made by autotrophs Plant Cell Communication Plants lack a nervous system; they’ve evolved hormones and chemicals as messengers *Learning objective: List 4 broad categories of plant responses to herbivory (and pathogens) and provide an example of each* 1. Intact and impenetrable barrier: serves as exterior/STRUCTURAL protection a. Ex) bark, waxy cuticle b. Thorns + springs (discourage animals by causing physical damage, inducing rashes/allergic reactions) c. Plant exterior can be compromised by mechanical damage, providing entry point for pathogens 2. Secondary metabolites: CHEMICAL compounds that are not directly derived from photosynthesis synthesis and aren’t necessary for respiration, plant growth, or development *Quiz question* a. May be toxic/lethal b. Alkaloids: discourage predators with noxious odors or repellant tastes. May cause excessive stimulation or lethargy (opioids) 3. Infected/surrounding cell death: in the damage tissue (and sites farther from injury location), defense reactions cause these cells to die, which stops the spread of the infection 4. Long-distance signaling: As tissue is damaged, jasmonates promote synthesis of toxic compound a. Jasmonates also cause synthesis of volatile compounds to attract parasitoids, to eventually kill the host (predator) b. Plant may activate abscission of injured tissue if damaged beyond repair *Learning objective: What techniques do plants use to avoid herbivory?* Apparency: hiding from herbivores Spatial refuges: areas physically inaccessible or hidden from herbivores (ex: plant growing in cliff) Temporal refuges: plants grow or flower when herbivores are inactive  Biotic refuges (associated resistance): reducing chance of herbivore finding nearby plants; masking scents, repelling herbivore, offering alternate food, and changing the environment, attracting predator of herbivore *Question: How do plants communicate that water levels are low?* cell-to-cell communication via hormones *Learning objective: How does one plant communicate with another plant?* Hormones: molecules that some cells use to tell other cells what to do ○ Plants: hormones move via tubes in circulatory system using gravity and transpiration ○ Humans: utilize a pump in the circulatory system (faster) Hormone secreting cell: Target cell: possesses specific receptors for a particular hormone Hormone receptor: on surface or within cell; binding of hormone to a receptor triggers a cascade of reactions that affect cell function Non-target cell: not affected by hormones Lipophilic messenger: diffuses across the membrane and combines with intracellular receptor proteins: when activated by the messenger, the proteins function as transcription factors (inducing transcription of new proteins) Ethylene: hormone gas that fruits release when they ripen, which encourages other fruits around them to ripen too ○ This is how ripening is coordinated at the same time  Gibberellin: (regulates)causes plants to stop devoting more energy into growth (leaves, height) and focus more on reproduction Shortstop: mixture of hormones used to slow down growth rate of plants (for less trimming, etc.) Abscisic acid: tells leaves that the plant is out of water (sometimes when there is actually water) ○ Made by roots and shoots upward. ○ Travels to guard cells…stomata close in response…photosynthesis stops… Action Potentials Central nervous system: ○ Brain and spinal cord Peripheral nervous system: ○ Peripheral nerves Presynaptic neuron: Postsynaptic neuron: Plasma membrane:  ○ Fluid mosaic model: the plasma membrane consists of many components—phospholipids, cholesterol, protein, carbohydrates—that gives membrane fluid character ○ Phospholipids: hydrophobic head and hydrophilic tails ○ Glycoproteins: carbohydrates attached to proteins on membrane’s exterior ○ Glycolipids: carbohydrates attached to lipids on membrane’s exterior *Question: How do neurons communicate?* One neuron receives and synthesizes messages (from other neurons) before “making a decision” to send the message on to other neurons Action potential: sudden, large, transient reversal in resting potential generated by sudden openings and rapid closings of ion channels ○ “All-or-nothing” response: once initiated, the action potential cycle goes all the way to completion—there is no “half” or “partial” Membrane potential: the difference in charge between the outside and inside of the cell ○ The lipid bilayer that surrounds the neuron is impermeable to ions; ions must pass through channels spanning the membrane ○ Voltage-gated ion channels: change their structure in response to voltage changes; regulate the relative concentrations of different ions inside and outside the cell 1. Resting potential: the difference in charge between outside and inside in a resting cell (+ outside = more Na+, - inside = K+ and - proteins) At rest, a difference in charge (inside and outside the cell) of about -70/80 mV is maintained ○ If membrane was equally permeable to all ions, system would reach equilibrium The voltage gated K+ channels and Na+ channels are closed The Na+/K+ pump is moving 3 Na+ outside for every 2 K+ inside ○ Active transport: pump requires energy/ATP from cellular respiration ○ Creates concentration gradient and difference in charge; a lot of Na + is pumped outside (more positive charge) and less K+ is pumped inside (relatively negative charge) The K+ and Na+ leak channels are always open ○ Na+ leaks inside, diffusing from high concentration to low concentration ○ K+ leaks outside, diffusing from high concentration to low concentration ○ There are much more K+ channels, so K+ diffuses outside cell faster; more cations are leaving cell then entering, so inside is negatively changed relative to outside ○ Na+/K+ pump maintains resting membrane potential (the NA+/K+ PUMP IS ALWAYS OPEN) 2. Depolarization: Stimulus from sensory cell/neuron (neurotransmitters binding to receptor) causes decrease in the difference in the voltages between outside and inside (depolarizing toward threshold potential) Na+ channels open up; A LOT of Na+ goes inside the cell along the concentration gradient ○ Inside of cell becomes more positively charged (+40 mV) Process continues until concentration gradient reaches a certain level and the Na+ channels close again 3. Repolarization: K+ channels open; A LOT of K+ goes outside the cell ○ now the K+ is outside and the Na+ is inside  ○ 4. Hyperpolarization: Inside of cell becomes EVEN MORE negative (magnitude < -80 mV) as K+ continues to leave the cell Process continues until the K+ is depleted, and the K+ channel closes 5. Recovery Na+/K+ pump is active again! THE NA+ GATED CHANNEL AND K+ GATED CHANNEL ARE CLOSED Return (very quickly) to resting potential *Question: How do you measure an action potential?* with an oscilloscope *Learning objective: Draw an action potential as visualized on an oscilloscope. Label each of the five phases. Discuss what is happening in terms of voltage-gated ion channels opening/closing at each point along the potential.*  Threshold: Undershoot: *Learning objective: Explain why action potentials propagate in only 1 direction down an axon* *Area behind currently occurring action potential CANT depolarize because the voltage-gated Na+ channels are INACTIVE there* *Learning objective: Explain (1) why action potentials propagate more quickly down myelinated axons and (2) the role played by nodes of Ranvier in this process.* For the action potential to communicate info to the other neuron, it must travel along the axon and reach axon terminals to initiate neurotransmitter release The conduction speed of action potential depends on axon diameter and axon resistance to current leak ○ Myelin acts as insulators; prevents current from leaving axon —> increases speed of action potential conduction Nodes of Ranvier: gaps in myelin containing voltage-gated Na+ and K+ channels ○ Flow of ions through channels regenerates action potential over and over again ○ If Nodes were not present, Na+ and K+ channels would need to continuously regenerate action potentials at very point (continuously) along axon (instead of specific points) —> action potential would propagate slowly Saltatory conduction: the jumping of the action potential along the neuron from one Node to the next Communication between neurons We are now looking at moving info from one neuron to another ○ Within a cell: fast ○ Between cells: slower Chemical synapse: 1. An action potential arrived at the axon terminal a. The triggers the voltage gated calcium (Ca2+) channels to open up 2. The Ca2+ enters the axon terminal a. An active pump pushes Ca2+ OUT, forming a concentration gradient; more Ca2+ outside than inside 3. Inside the axon terminal, the Ca2+ interacts with the synaptic vesicles and the neurotransmitters (cell-unique chemical) within  a. The neurotransmitters/vesicles (?) move to the end of the axon terminal, merge with the terminal, and dump their contents into the synapse 4. The neurotransmitters diffuse across the synapse and bind to ligand-gated ion channels on the postsynaptic membrane a. This will cause the ion channels to either open or close, depending on the neurotransmitter 5. If the binding of the neurotransmitter opens the ligand-gated ion channels, then graded potentials (?) are formed a. Ligand-gated ion channel: triggered by specific chemical, not electrical/voltage charge b. Neurotransmitters can make the postsynaptic neuron more likely to undergo action potential *Learning objective: Summarize the main mechanisms by which neurotransmitters are cleared from the synaptic cleft and explain why this is important* 6. Terminating the signal and returning to initial conditions, to prepare for a new signal!— a. Reuptake by the presynaptic neuron: channels open up in the presynaptic neuron to allow the neurotransmitter to diffuse inside (and be reused)  b. Enzymatic degradation: presynaptic neuron dumps enzymes into synapse to break down neurotransmitters c. Diffusion reduces neurotransmitter levels: neurotransmitters diffuse away from the synapses and eventually break down *Learning objective: Predict the consequences if neurotransmitter was NOT rapidly cleared from the synapse.* Increased neurotransmission at synapses that release neurotransmitter ○ Then, neurotransmitter stays in synapse and continually bind/unbind to postsynaptic receptors *Learning objective: Diagram the series of steps that leads to neurotransmitter release at the motor neuron axon terminal. Describe how the synaptic release of acetylcholine molecules can lead to the firing of muscle action potentials.* Acetylcholine (Ach): neurotransmitter ○ Helps skeletal + smooth muscles contract ○ Reduced contractions of cardiac muscles *Learning objective: Discuss how one neurotransmitter can be both excitatory and inhibitory.* Excitatory neurotransmitter:  Inhibitory neurotransmitter: The same neurotransmitter can have different effects depending on the RECEPTOR itself ○ Release of neurotransmitter at excitatory synapse causes excitatory postsynaptic potential (EPSP): makes postsynaptic neuron more likely to fire an action potential ○ Release of neurotransmitter at inhibitory synapse causes inhibitory postsynaptic potentials (IPSPs): a hyperpolarization of presynaptic membrane, making neuron less likely to fire action potential ○ Ex) Acetylcholine (Ach) in a motor neuron to a skeletal/smooth muscle has an excitatory effect (more likely to contract), Ach in a motor neuron to cardiac muscle has an inhibitory effect (less likely to contract) *Learning objective: Predict what happens to membrane potential when a neuron is exposed to an excitatory vs an inhibitory neurotransmitter* The inhibitory neurotransmitter helps in deciding ‘the brain doesn’t need to know/sense this’, so the action potential stops here Summation: Several presynaptic inputs of EPSPs (multiple bursts of neurotransmitters having a singular effect) released into the substance until enough to sufficiently depolarize postsynaptic neuron and trigger the action potential ○ Occurs at the axon hillock ○ The postsynaptic neuron’s threshold for action potential is VARIABLE—it can be manipulated! ○ Synaptic summation and the threshold for excitation act as filter so that random “noise” in the system is not transmitted as important info Multiple neurotransmitters (from multiple presynaptic neurons) can be dumped into the synapse at once  Temporal summation: 2 excitatory neurotransmitters came from the same presynaptic neuron (rapidly occurring neurotransmitters at single synapse) Spatial summation: 2 excitatory neurons came from different presynaptic neurons (neurotransmitters are applied at same time but at different areas, w a cumulative effect) Natural toxins: evolutionarily take advantage of our nervous system *Test question: If there was a toxin that blocks Ach receptors, how would that induce death in humans?* Diaphragm (smooth muscle) becomes paralyzed, causing suffocation Sensory Input We have 5 primary senses but also… ○ Vestibular sensation: an organisms sense of spatial position and balance ○ Proprioperception: position of bones, joints, and muscles 3 steps in sensory perception 1. Reception: how we receive the stimulus and translate it into action potentials a. The activation of sensory receptors by stimuli 2. Transduction: moving the action potential to the central nervous system a. Converting a stimulus into an electrical signal in the nervous system 3. Perception: an individual's interpretation of a sensation (in the brain) Reception— *Learning objective: Explain how physical sensation is received and transduced in animals.*  Receptive field: the region in space in which a given sensory receptor can respond to a stimulus Mechanical Reception: possesses specialized membranes that respond to pressure Receptor potential: the change in electrical potential produced ○ Graded potential: the magnitude of these potentials (that cause depolarization) varies w the strength of the stimulus Mechanoreceptors: ○ Tectorial membrane: ○ Tether: filament/string anchoring channel to tectonic membrane or cytoskeleton ○ Cytoskeleton: small filaments that help maintain cell structure ○ There is a concentration gradient of cations (higher concentration outside the cell than inside), implying some sort of “resting potential” Implies existence of pump ○ Once there is sensory input… 1. The tectorial membrane moves in response to the stimulus 2. The tether moves to one side, pulling the channel open 3. The cations go down the concentration inside the cell, making the inside more positive 4. Action potential! *Learning objective: Explain why hearing is the result of a mechanical stimulus.* Quick answer: vibrations through air and the movement of hair cells is mechanical Hearing with mechanoreceptors— 1. Sound moves through the air, causing vibrations a. Differences in vibration means different ways ear is impacted 2. Moving air molecules go to the middle ear (ear canal) 3. Makes the eardrum (tympanic membrane) vibrate (differently for each sound) 4. Causes the (little bones) to vibrate 5. Moves past other membrane to the cochlea (saltwater inside begins to vibrate) a. Cochlea structure is important to distinguishing sound; the different widths (large to narrow) of the cochlea spiral receive different vibrations b. The brain is able to know which sounds/signals came from which part of the cochlea BECAUSE… Inside the cochlea are mechanoreceptors! 1. The tectorial membrane is moved by the vibrations 2. The hair cells are moved a. Hair cells have set of projections called STEREOCILIA that open ION CHANNELS when they bend b. Volume of sound is determined by how many hair cells at a particular location are stimulated 3. Action potential sent to brain Flow of information of mechanical reflex: Stimulus, receptor protein, ion channel, action potential, neurotransmitter release *Learning objective: Predict what would happen to hearing/audition given a scenario (e.g., ear canal is stuffed with cotton, stapes is removed, middle ear is full of fluid)* Perception is reduced! Chemical reception: 1. Ligand molecule binds to first cell 2. Action potential ensues 3. Neurotransmitter released to second cell 4. Message sent to brain Chemoreceptors: 1. Sensory neurons in nose/tongue have channels for different (specific) odor/taste molecules a. Molecule binds + opens ion channel b. Action potential initiated c. Brain recognizes odor/taste molecules (ex: garlic/pepper) Olfactory epithelium: collection of specialized olfactory receptors ○ Olfactory neurons are bipolar: one part reaches to detect the stimulus, the other sends signals to the brain ○ Taste bud: cluster of gustatory receptors located within the bumps of the tongue Some individuals may have better senses of smell than others due to… ○ Possessing more of the sensory neurons for a specific odor ○ Possessing a greater variety of receptors for different odors  83. Compare and contrast the chemoreception that occurs at synaptic junctions and with smell and taste. 84. Explain how smell is received and transduced. 85. Predict what would happen to smell given a scenario (e.g., stuffy nose, damage to olfactory neurons) 86. Explain how taste is received and transduced. 87. Predict what would happen to taste given a scenario (e.g., burn tongue on hot food) 88. Predict what would happen if action potentials generated from taste buds traveled to the visual processing region of the brain. 89. Identify adaptations of wolves and moose that make their senses different from ours. Perception— When they first arrive at the brain, all action potentials initially “appear” the same *Question: How are all of these different electrical signals distinguished?* 1. Which sensory neuron is stimulated? a. The brain knows where the signal came from and keeps track (which receptors) 2. Number of action potentials per neuron a. Strong signal: action potentials occur over and over again (lots in rapid succession) 3. How many neurons are firing? a. Big impact: lots of neurons involved Thalamus: clearinghouse of most sensory information ○ Interprets where the signal came from and ROUTES it to appropriate area of the cortex based on the signal’s TYPE ○ Somatosensory processing region: touch/feel ○ Auditory processing region: sound ○ Visual processing region: sight  1 BIOL 112 Test 3: Viruses and Evolution Intro to Viruses Virus: infectious obligate, intracellular parasite comprising genetic material (DNA or RNA) surrounded by a protein coat ○ Infectious = likely to spread or influence others in a rapid manner. ○ Obligate = restricted to a particular function or mode of life. ○ Intracellular = located or occurring within a cell or cells. ○ In terms of symbioses, the virus is an example of parasitism Viral replication— 1. Attachment: Virus recognizes and attaches to specific living cell (after floating/bumping around) a. Attaches via proteins in the capsid or glycoproteins embedded in the viral envelope b. Requires lots of virus to increase chance of getting sick (so virus can find correct cell) c. *Quiz question:* Viruses can only attach to cells that have specific viral receptor molecules on their surface 2. Entry: a. Cell is ‘tricked’ into opening up and DNA is allowed to enter 3. Replication: Virus copies its genome and manufacture its own proteins a. Virus uses the cell’s machinery to replicate its DNA… 4. Assembly: Newly made virus particles are assembled into capsids a. Making materials needed for replication (nucleic acids, proteins, etc.) 5. Release/Egress: Progeny virions escape host cell so they can infect other cells a. Lysis: b. Apoptosis: c. Budding:  2 Host: An organism that is infected with or is fed upon by a parasitic or pathogenic organism; An organism that another organism uses to be able to survive and reproduce ○ Viruses can infect into certain species of hosts and only certain cells within that host ○ Permissive: specific host cells that a virus must occupy and use to replicate—specificity due to viral receptor Bacteriophage: viruses that infect bacteria cells X *Question: Are all viruses bad?* Bacteriophages: ○ Fight the bacteria that make us sick Virus Classification Virus are hard to classify bc viruses have no common genomic sequence that they all share BUT they all share— ○ Possess surface proteins that latch onto particular molecules to find the correct receptor in a host cell Those that don’t find the correct target cell will eventually destruct —> so even if we have the virus in our body it doesn’t mean we will be infected  3 What makes something alive? 1. Has cells 2. Reproduces 3. Performs respiration 4. Maintains homeostasis 5. Has genetic material 6. Evolves *Learning objective: Compare and contrast a bacterial infection (like LD) to virus* LD System COVID-19 System Host: white-footed mice, deer, birds, etc. Host: humans, bats, livestock, etc. Vector: Ixodes ticks carrying Borrelia Vector: no living vector— infectious particles in airborne droplets Pathogen: Borrelia burgdorferi Pathogen: SARS-CoV-2 *Learning objective: Discuss how climate change impacts the geographic distribution of viruses*  4 Distribution of Vectors: the viability for the compactness of the virus is enhanced in warmer climates, ex) West Nile virus ○ Asian tiger mosquito is a vector for dengue fever, Japanese encephalitis, yellow fever, West Nile virus, St. Louis encephalitis, and LaCrosse encephalitis (?) Distribution of Hosts: ? ○ With ice melting, Pacific harbor seals and otters are getting phocine distemper virus from Atlantic seal populations  5 *Learning objective: Describe what selective pressures organisms experience in a symbiotic vs predator/prey vs competitive relationship* In a symbiotic relationship, selective pressures push organisms to evolve traits that enhance the mutual benefit they receive from their partner, while in a predator/prey relationship, the selective pressure is on the prey to avoid being eaten and on the predator to become more efficient at capturing prey, and in a competitive relationship, the pressure is on organisms to acquire resources more effectively than their competitors, often leading to specialization in resource use Review of COVID-19 Caused by SARS-CoV-2 virus ○ Coronavirus disease 2019 ○ RNA virus First known case: Wuhan, China December 2019 Comes from well-known family SARS virus—similar diseases already were being studied ○ Occur in number of animal species *Quiz question*: COVID is evolving, even though viruses aren’t alive ○ *Quiz question: The very large # of COVID infected hosts means that—* SARS-CoV-2 was likely to evolve rapidly and adapt quickly to its new host 1. Starts with droplets from cough, sneezes, or breath (also singing or speaking) 2. Virus gets to mucous membranes throat 3. Latches its surface proteins to ACE2 surface protein receptors on healthy cells (especially in lung) a. Presence of ACE2 receptors can depend on age  6 Zoonoses: ○ COVID probably originated from bats ○ As a natural zoonotic spillover event in an outdoor food market in China, mostly likely from a virus that occurred in raccoon dogs (Nyctereutes procyonoides) ○ Salmonellosis, West Nile virus, SARS, HIV, plague, rabies, LD, etc. ○ 6/10 infectious diseases in humans are zoonotic  7 ○ ○ What factors are increasing zoonosis emergence? 1. Deforestation and other land use changes 2. Illegal and poorly regulated wildlife trade 3. Intensified agriculture and livestock production 4. Antimicrobial resistance 5. Climate change COVID-19 Pneumonia: Virus spreads down respiratory tract to lungs ○ Lower pathways have more ACE2 receptors than rest of respiratory tract ○ COVID more likely to go deeper than viruses like those causing common cold ○ As in other pneumonia-causes: 1. Lungs become filled with fluid and inflamed 2. Leads to breathing difficulties 3. Sometimes severe enough to require hospital treatment with oxygen or ventilator ○ Most severe symptoms associated with overactive inflammatory immune responses ○ Common pattern: overactive immune response Allergies, asthma, COVID These strange responses may be due to genetic mutation, exposure,  8 *Question: What happens when COVID enters the lungs?* Respiratory System We move air in and out of our lungs so we can have oxygen and carbon dioxide for cellular respiration 1. Trachea, bronchus, bronchioles 2. Alveolus, alveolar epithelium, tissue fluid, capillary endothelium 3. Plasma, red blood cell membrane, hemoglobin a. Gas exchange occurs very fast i. Alveoli are in direct contact with the capillaries; oxygen diffuses from alveoli into the blood (move to body cells); carbon dioxide will diffuse from the blood into the alveoli (to be exhaled) ii. Large SA and thin-walls of alveoli sacs facilitate easy gas exchange Fick’s Law of Diffusion determines how fast/efficiently gas exchange can occur  9 Q: Rate at which gas diffuses between 2 points ○ We want this to be high! Needs to be maximized for life-sustaining processes D: Diffusion coefficient ○ Pretty much fixed, can’t really modify (evolutionarily set) ○ Which gas Oxygen, carbon dioxide ○ Which medium will the gas diffuse in? Extracellular fluid in alveoli sac: mostly water (molecule dissolves) ○ Temperature Standard body temperature in alveoli A: Surface area across which the gas diffuses ○ Interior of the alveoli sphere—spheres have the maximum surface area for the space it occupies (optimal design for maximizing surface area)! ○ This should be high! P1 - P2: Difference in partial pressure of the gas at the 2 points ○ Difference between concentration of oxygen gas in alveolus (P1) and concentration in blood stream (P2)  10 ○ In order to facilitate diffusion, we want this difference to be larger ; the bigger the difference, the faster the diffusion ○ We can manipulate this by increasing P1 or decreasing P2 L: the distance between the 2 points (start point and end point) ○ DISTANCE OVER WHICH GAS DIFFUSES FROM P1→P2 ○ Start point: Interior of sac, edge of first cell ○ End point: when it enters the bloodstream (in the capillary or attached to red blood cell) ○ We want to minimize this distance; the shorter the distance the faster the diffusion takes *Test question: Which part of this equation would be affected by mountain climbing at a high altitude?* P1 P1 is the concentration of oxygen in the alveolus, and we get this oxygen from breathing in the air available to us. Since oxygen is scarce in higher altitudes, P1 would be lower. As a result, Q (rate of diffusion) would be lower as well. ○ To adjust for this, mountain climbers will breathe oxygen from their air packs (compensating for lack and increasing P1)  11 ○ *Climbers will camp in certain altitudes for weeks: this changes the set point, and more red cells are adjusted to be in the blood. *P2 is altered: as soon as oxygen enters the blood, a red blood cell will immediately be there to carry it (due to its higher concentration in the blood). However, crowding of red blood cells in the bloodstream will make it more difficult to push (water?) through; hard on the heart (makes it work harder) Some human population have adapted to living at high altitudes 1. Increased lung capacity 2. Higher red blood cell count (and they don’t pay the heart price) 3. Modified hemoglobin-oxygen binding affinity 4. Various mutations of EPAS1 gene *What are we affecting with COVID/ Implication of Fick’s Law with COVID* Alveolar sac starts to fill up with fluid ○ A/Surface Area: there is less area in which diffusion can occur; less of interior alveolus is exposed ○ L: because of the fluid, the oxygen molecules have to travel longer distances (slower, every breath is less productive) ○ D: the fluid medium is much harder for the oxygen to diffuse through (slower) ○ We need to manipulate P1! If put on a ventilator, the patient receives more oxygen to enter the lungs/alveoli—so P1 increases, and therefore Q is raised Population Genetics Focusing on hosts and vectors (living things), and not viruses (nonliving) Gene: basic unit of heredity— specific DNA segment that codes for a functional molecules ○ A distinct sequence of nucleotides forming part of a chromosome Humans have ~20,000 genes and ~500,000 proteins ○ Arise due to mutations ○ *Question: Do we all have the same genes* No, almost. Example: genes carried on X vs genes carried on Y  12 BUT we (or any species) share A LOT of the same ones (99.999%), just w different allelic forms ○ Genetic variation: Allele: a variant (difference versions) of a gene; arose due to mutations ○ Allelic variation: Allele frequency: ○ This bunny population has 2 alleles: G and g (diploid) When a gene has multiple alleles, we write: A1, A2, A3… Homozygous: (GG, gg) Heterozygous: (Gg) Dominant allele: (G) ○ Incomplete dominance: ○ Different allele combinations that don't follow the dominant/recessive system: A1A2, A1A3,… Recessive allele: (g) *Question: How many G alleles are there out of all the G and g alleles in the population?* f(G)=11/20, f(g)=9/20  13 Genotype: genetic information— set of information to make proteins ○ The more alleles there are, the more genotypes there are ○ Phenotype: physical trait/morphology— determined by/coded by genotype ○ Behavior; example) yawning, reactions ○ Physiology; example) blood type, alcohol tolerance ○ Individuals in a population have different phenotypes because they have different variants (alleles) of the same genes; that is, they have different genotypes  14 *Question: How do allele frequencies change over time/generations?* *Question: What can cause allele frequencies to change over time?* 1. Mutation: a change in DNA— the ultimate source/foundation of new alleles a. Needed for the other 3 mechanisms for changes in allele frequencies to occur! Mutations are responsible for every bit of genetic variations in the world b. Slow changers of allele frequencies— especially in species with a large population  15 Point mutations: ○ Most common because they are very small (harder to detect, cell is less likely to repair) ○ A change in base pair sequence can cause… 1. Abnormal protein that doesn’t function 2. Inability to transcribe protein 3. Normal protein is produced (different sequences can sometimes code for the same protein) 4. A similar protein that can still perform its original function (better or worse) a. Very rare for it to beneficial (more likely for random mutation to be worse), but occurs enough times through generations b. Ex) Single point mutations: Sickle cell anemia, Huntington disease, Cystic fibrosis. Series of mutations: Cancer! ○ 2. Gene Flow/Migration: movement of different alleles from one population to another a. Requires that the two populations interbreed when the new allele is introduced! Example: ticks using birds/deers to travel long distances and introduce new alleles to a population and reproduces Example: wolves who cross the ice bridge into Isle Royale introduce new alleles and reduce interbreeding (join population and helps it to grow again) ○  16 ○ Several genes have no genetic variation in the population at all! (shown by gaps/windows in the data) 3. Genetic Drift: changes in allele frequencies due to chance event a. The key feature is chance! Random event! b. Drift is a function of population size: FAR more likely to affect small populations (bigger—>likelihood of drift goes down—mutations counteract) c. The longer a population experiences drift, the more genetic variation it loses Founding events: few member of the original population starting a new population/colony in a new place (change in population over DISTANCE) 1. Colony will have reduced genetic variation from the original population 2. Colony will have a non-representative sample of the genes in the original population ○ Founder Effect: event that initiated an allele frequency change in part of the population, which is not typical of the original population the small population that survives the event will expand and its descendants will all have the genes If you have one ancestor with a particular gene, all the descendants will have that particular gene too (future generations resemble their parents) ○ The size of the sample (new founding population formed) determines if the amount of genetic variation is maintained or reduced Bottleneck events: an extreme example of genetic drift that happens when the size of a population is severely reduced ; magnification of genetic drift as a result of a natural catastrophe ○ the population stays in place (change in population over TIME) ○ For a number of generations the population remains small, then grows —> genetic variation still remains small! Can be solved by 1. Appearance of new mutations (will take a LONG time) 2. New population introduced  17 *Quiz question: What bottlenecks and founder effects have in common is that—* 1. They are both examples of genetic drift 2. They both involve multiple generations of small populations 3. They are events that are very likely to result in evolution 4. Natural Selection: Increase in frequency of a particular allele (and decrease of other alleles) because individuals with the particular allele are more likely to survive and reproduce a. The more prolific reproduction of individuals with favorable traits that have survived environmental changes because of those traits i. Involves differential reproductive success b. Not random at all! Has to occur if the population has— i. Variation in a trait (genetic variation already exists) ii. Fitness differences (relationships between trait and some aspect of reproduction or survivorship) iii. Heritability of trait (must be at least partially heritable) c. Leads to adaptations: heritable traits that—if an individual happens to have them—support the individual’s survival and reproduction i. Leads to descent with modification d. Artificial selection: the identification by humans of desirable traits in plants and animals, and the steps taken to enhance and perpetuate those traits in future generations (Man-made allele frequency changes) e. *Quiz question: Statements like ‘the bacteria evolved resistance because they were exposed to an antibiotic’ are incorrect because—* The variation that natural selection works on is already in a population and doesn’t arise in response to an environmental change  18 *Test question: Why would there be mosquito individuals who were resistant to the DDT chemical before it was created* A random mutation existed that caused resistance and persisted, and was revealed when the selection pressure was applied. Evolution: A change in allele frequencies in a population over time Major unifying principle in biology; Darwin argued that differential survival and reproduction among individuals in a population (= natural selection) could account for much of the evolution of life Natural selection is the most popular cause of evolution; leads to populations of organisms where most individuals have adaptations: structural, physiological, or behavioral traits that enhance an organism's chances of survival and reproduction (i.e. fitness) ○ Evolution requires the same 3 factors as natural selection to occur  19 Researchers expected any evidence of evolution (changes in any trait) to take A LONG TIME to appear ○ A serious drought occurred, causing plants to halt photosynthesis and stop making seeds, limiting the finches’ food source ○ This shifts the break size distribution to the right, because larger beaked finches were able to find and break big seeds that the other finches haven’t gotten to yet ○ Example of natural selection (and evolution)!  20 The next year, rain came again, photosynthesis resumed, and the beak size distribution shifted back *Question: Does short-term changes in beak size matter?* Recent work suggests new species can be formed when no more than 3 drought years occur back to back ○ Drought creates intense selection on beak size, where beak size determines song—song would sound so different from other species, wouldn’t mate Adaptations come with trade-offs ○ Male frogs with larger throats sacks can make louder sounds to attract a mate and reproduce BUT may attract a predator and uses up a lot of energy —> don’t live as long  21 ○ Make birds with larger throat patches attract more females BUT makes them easier to get punctured by bushes and uses up a lot of energy ○ This occurs is viruses too— Virulence: how sick a virus a makes you, dramaticness of symptoms COVID has traded virulence for Ease of Transmission to make more copies of itself Adaptation vs Acclimation ○ Adaptation: a genetic trait that gives an advantage to an individual in a group over another individual—not reversible