FINAL EXAM: BISC 12 Study Guide Midterm 2 Chapter 54 (1-2)---Community Ecology o Interspecific interactions- interactions with other species

s Competition (-,-) Competitive Exclusion- G.F. Gause- two species cannot coexist permanently in the same community if their niches are identical o One species will use resources more efficiently and thus reproduce more rapidly which this slight reproductive advantage will eventually lead to the local elimination of the inferior competitor. Ecological niche- sum of a species use of biotic and abiotic resources in its environment Resource partitioning- the differentiation of niches that enables similar species to coexist in a community (species modify their niches to survive- natural selection) Fundamental niche- the life pattern that the organism should have under ideal conditions Realized niche- the life pattern that the organism actually assumes due to scarcity competition, etc Allopatric- geographically separate Sympatric- geographically overlapping Character displacement- the tendency for characteristics to diverge more in sympatric populations of two species than in allopatric populations of the same two species Predation (+,-) Adaptations are seen from both predator and prey o Cryptic coloration- camouflage o Aposematic coloration- warning coloration o Batesian mimicry- a palatable or harmless species mimics an unpalatable or harmful model To work the predator must be able to learn to recognize the model and the model needs to outnumber the mimic o Mullerian mimicry- two or more unpalatable/harmful species resemble each other (advantage if the more unpalatable prey

there are, the more quickly the predator learns to avoid them) ***Predators also use mimicry snapping turtles tongue looks like worm Herbivory (+,-) Most herbivores are actually invertebrates (grasshoppers and beetles) Predators adapt- chemical sensors to tell toxicity, sense of smell, eating only specific parts like flowers Prey adapt- plants arsenal includes- chemical toxins and structures such as spines and thorns Symbiosis- two or more species live in direct and intimate contact with one another Parasitism- (+, -) one organism (parasite) derives its nourishment from another organisms (host), who is harmed in the process o Endoparasites- within the body of the host (tapeworms) o Ectoparasites- feed on the external surface of the host (lice) o 1/3 of all species are parasites o Significantly affect the survival, reproduction, and density of their host population, directly or indirectly Mutualism/Mutualistic symbiosis- (+, +) o Obligate mutualism- at least one species has lost the ability to survive without its partner o Facultative mutualism- both species have ability to survive alone, but benefit from the other Commensalism- (+, 0)o Difficult to document because any close association usually affects both species (if only slightly) o Hitch-hikers such as algae and barnacles, usually considered commensal, but may slow down whale/turtle and provide camouflage o Secondary compounds- chemicals that arent part of metabolism for plants but used as defense (also in bees, etc) o Intraspecific interactions interactions within a single species o Species Diversity- the variety of different kinds of organisms that make up the community Species richness- the number of different species in the community Relative abundance- the proportion each species represent of all individuals in the community

o o o

Shannon diversity (H): H= -[(pA ln pA)+ (pB ln pB)+( pC ln pC)] o ABC= species p= relative abundance Trophic Structure- feeding relationship between organisms (movement of energy and matter through an ecosystem) Primary Producers- plants and other autotrophs Primary Consumers- herbivores Secondary consumers- carnivores Tertiary/quaternary/etc- carnivores Decomposers Charles Elton- food web- interconnected feeding relationship (diagrammed by who eats whom) A given species can weave into the web at more than one trophic level (omnivores) Humans are the most versatile omnivores Two ways to simplify food webs 1) Group species with similar trophic relationships in a given community into broad functional groups (ex. 100 phytoplankton are grouped as the primary producers) 2) Isolate a portion of the web that interacts very little with the rest of the community Food chains are relatively short (rarely more than 7 links, usually >5) Energetic hypothesis- length of the chain is limited by the inefficiency of energy transfer along the chain (only 10% of the energy stored in the organic matter of each trophic level is converted to organic matter at the next trophic level) Dynamic stability hypothesis- long food chains are less stable than short food chains Population fluctuations at lower trophic levels are magnified at upper levels, potentially causing local extinction of top predators, longer food chains are the more slowly top predators can recover from environmental setbacks *** Most data supports energetic hypothesis Dominant Species- those species in a community that are the most abundant or that collectively have the highest biomass Biomass-the total mass of all individuals in a population Exert a powerful control over the occurrence and distribution of other species Why a species becomes dominant Competitively superior in exploiting limited resources Most successful at avoiding predation or the impact of disease

o Keystone species- not necessarily abundant in a community but they exert strong control on community structure by their pivotal ecological roles or niches. Identified by removal experiments Help maintain the diversity of a community o Foundation species/ ecosystem engineers- alter their physical environment on a large scale through their behavior or their large collective biomass (ex. beaver) Facilitators- positive effects on the survival and reproduction of other species o Bottom-up model- VH - unidirectional influence from lower to higher trophic levels If you add predators or remove predators from this community the effect should not extend down to the lower trophic levels o Top-down model (aka trophic cascade model)- postulates that predation mainly controls community organizations because predators limit the number of herbivores, herbivores limit plants, and plants limit nutrient level Biomanipulation-attempt to prevent algal blooms and eutrophication by altering the density of higher level consumers in lakes instead of chemical treatment Chapter 55 (4-5) o Life on earth depends on the recycling of essential chemical elements (scarcity) o Biogeochemical cycles- any of the various chemical cycles that involve both biotic and abiotic components. Global- gaseous forms of carbon, oxygen, sulfur, and nitrogen occur in the atmosphere Local-other elements like phosphorus, potassium and calcium are to heavy to occur as gas so cycle more closely o Decomposition is controlled by factors such as temperature moisture, and nutrient availability. Usually grow faster and decompose material more quickly in warmer temperatures Tropical rainforest-organic material decomp in few months/years (75% of nutrients in ecosystem are in the woody trunks of trees, 10% in soil)--- result of short cycling time Temperate forest- organic material decomp in four to six years (as much as 50% in soil) o Result of higher temperatures and more rain in rainforest o Most chemical cycles are now influenced more by human activities than by natural processes

o o

Human activity often removes nutrients from one part of the biosphere and adds them to another Nitrogen is the main nutrient lost through agriculture agriculture has a great impact on the nitrogen cycle Human activity has more than doubled Earths supply of fixed nitrogen available (with industrial fertilizer providing the largest additional nitrogen source) Nitrogen enters ecosystem as nitrate (sometimes ammonium) Fossil fuel combustion and increased cultivation of legumes also increases nitrogen levels Critical load- the amount of added nutrient (usually nitrogen of phosphorous) than can be absorbed by plants without damaging the ecosystem integrity. Nutrient runoff can also lead to the eutrophication of lakes Eutrophication- the addition of nutrients and artificial/nonartificial substances through fertilizers and sewage into any habitat Usually referring to lakes, oceans, etc. which results in the blooms of phytoplankton The burning of wood and fossil fuels (coal and oil) release oxides of sulfur and nitrogen that react with water in the atmosphere to form sulfuric acid and nitric acid. Creates precipitation that has a pH less than 5.2 This lowers the pH of streams and lakes and effects soil chemistry and nutrient availability Occurring since the Industrial Revolution Acid precipitation is a regional problem arising from local emissions 1980- pH of precipitation in N. America and Europe averages 4.0-4.5 Causes calcium and other nutrients to leach from the soil, which affects the health and growth of plants Can also directly affect plants by leaching nutrients from their leaves Freshwater ecosystems with low concentrations of bicarbonate are the most readily damaged by acid precipitation Experiments being carried out to test the feasibility of reversing effects of acid rain are the Hubbard Brook idea of CA+2 addition and covering a forest with a glass roof and showered the forest with clean precipitation Sulfur dioxide emissions decreased 31% in the US between 1993 and 2002, but nitrogen oxides are increasing Biological magnification- a process in which retained substances become more concentrated at each higher trophic levels in a food

chain (ex. mercury which is turned into methylmercury)top-level carnivores tend to be the organisms most severely affected by toxic compounds Chlorinated hydrocarbons (PCB) and pesticides (DDT) DDT involved in decline of pelicans ospreys and eagles because it interfered with the deposition of calcium in their eggshells so when parent would sit on eggs, they would break- Rachel Carson Silent Spring o Concentrations of CO2 in the atmosphere have been increasing from fossil fuels and deforestations by about 40% from the mid-19th century, if this continues then by 2075 the concentration will be more than double than it was at the start of the Industrial Revolution Increased productivity of plants is on predictable consequence of increasing CO2 levels (help C3 species like wheat and soybeans when today C4 like corn are usually favored) FACTS-I: Forest-Atmosphere Carbon Transfer and Storage (1995)- experiment at Duke University to assess how the increasing atmospheric concentrations of CO2 might affect temperate forests by manipulating the concentration that trees are exposed to Increase CO2 plots produced 15% more wood each year o Greenhouse effect- the warming of Earth due to the atmospheric accumulation of carbon dioxide and certain other gases, which absorb reflected infrared radiation and reradiate some of it back toward Earth Support for this is the correlation between CO2 levels and temperatures The ecosystem where the largest warming has already occurred is those in the far north, particularly northern coniferous forests and tundra. Analysis of fossilized pollen indicates that plant communities change dramatically with changes in temperature Many organism, especially plants, cannot disperse rapidly over long distances may not be able to survive the high rates of climate change projected, especially because many habitats are more fragmented than they were in the past limiting migration o Earth is protected from the damaging effect of UV radiation by a layer of ozone molecules O3 located in the stratosphere (17-25 km above Earths surface) Thinning since mid 1970s Results from accumulation of chlorofluorocarbons (CFCs) used to be in refrigerators and manufacturing CFCs rise to stratosphere and react with ozone reducing it to molecular O2 subsequent reactions liberate the

chlorine allowing it to react with other ozone chain reaction Most apparent thinning over Antarctica in spring At the more heavily populated middle latitudes, ozone levels decreased 2-10% in the past 20 years Decrease in ozone levelsincrease in intensity of UV rays UV radiation can cause DNA damage 1987- 190 countries signed the Montreal Protocol that regulates the use of ozone-depleting chemicals Many countries banded production of CFC o Even if CFC were globally banned today, the chlorine already in the atmosphere would continue to influence stratospheric levels for at lease 50 years. Chapter 56 (2-3, 5) o Conservation at the population and species levels Small-population approach Declining population approach o Small population approach Study the process that causes extinctions once population sizes have been severely reduced Extinction vortex- a downward population spiral in which inbreeding and genetic drift combine to cause a small population to shrink and, unless the spiral is reversed, to become extinct (positive-feedback loops) Key issue is the loss of genetic variation necessary to enable adaptations to environmental change In some rare cases, low genetic diversity has not impeded population growth (northern elephant seals with only 20 individuals- bottleneck effect) Minimum viable population (MVP)- the minimal population size at which a species is able to sustain its numbers and survive Often used in population variability analysis to predict a populations chances of survival over a particular time interval o One of first viability analysis on grizzly bears Effective population size- based on the breeding potential of the population Ne = (4Nf Nm)/(Nf + Nm) Nf =number of females Nm = number of males This effective population is equal to the idealized population if every individual breeds and the sex ratio is 1:1 o Declining Population Approach-

Focuses on threatened and endangered populations that show a downward trend, even if the population is far above MVP Different than small population approach because: Small population emphasizes smallness itself as an ultimate cause of a populations extinction (especially through loss of genetic diversity). Declining population approach emphasizes the environmental actors that caused a population decline Requires evaluation on a case to case basis o Weighing Conflicting Demands Habitat use is almost always the issue Mining jobs or habitat for timber wolves and grizzly bears? Because we wont be able to save every endangered species, we must consider the ecological role and determine keystone species to save Conservation must look at the whole community/ecosystem not just a single species o Sustainable development- development that meets the needs of people today without limiting the ability of the future generations to meet their needs o Sustainable Biosphere Initiative- Ecological Society of America- to define and acquire basic ecological information needed to develop, manage and conserve Earths resources are responsibly as possible. Lecture Life is o o o o o o o

Order Adaptation Response to stimuli Homeostasis Metabolism Reproduction Growth and development ***Does not require oxygen

Population- a group of individuals (aka subset of a species) of the same species occupying a given area Community- all the organisms that inhabit a particular area (living close enough for potential interaction) Ecosystem- all biotic and abiotic factors Biosphere- largest category, all ecosystems, aka Earth Scientific Law vs. Theory o Scientific Law- description of an observed phenomenon (Newtons Law of Gravity- Falls) o Scientific Theory- explanation behind the observed phenomenon Hypothesis can never be proven right o Reject or Fail to Reject Batesian mimicry- a type of mimicry when a harmless species looks like a species that is poisonous or unpalatable (different snakes) Mullerian mimicry- mutual mimicry by two dangerous/unpalatable species (bees, wasps, etc.)

Chapter 1---Study of Life Evolution- the process of change that has transformed life on Earth from its earliest beginnings to the diversity of organisms living today, it is the fundamental organizing principle of biology and the main theme o Creates diversity Biology- the scientific study of life, posing questions about the living world and seeking scientific base answers are the central activities Emergent properties- new properties that arise with each step upward in the hierarchy of life, owing to the arrangement and interactions of parts as complexity increases o Not unique to life Discovery science (descriptive science)- describes natural structures and processes as accurately as possible through careful observation and analysis of data. Chapter 52---Ecology and the Biosphere Ecology- (oikos- home + logos-study) the scientific study of the interactions between organisms and the environment o Environment influences organisms and organisms influence their environment o Study of the abundance and distribution of organisms o Roots are in discovery science o Henry David Thoreau- coined the term ecology Different levels of Ecology o Organismal- concerned with how an organisms structure, physiology, and behavior meet the challenges posed by the environment o Population- analyzes factors that effect population size and how +why it changes through time

o Community- how interactions between species affect community structure o Ecosystem- emphasizes energy flow and chemical cycling between organisms and the environment o Landscape- focuses on the factors controlling exchanges of energy, materials, and organisms across multiple ecosystem o Global- how the regional exchange of energy and materials influences the functioning and distribution of organisms across the biosphere Biotic factors- living factors- all organisms that are a part of the individuals environment Abiotic factor- nonliving factors- all the chemical and physical factors, such as temperature, light, water, and nutrients, that influence the distribution and abundance of organisms Species transplant o used to determine if dispersal is a key factor limiting the distribution of a species o to be successful, some organisms must not only survive in the new area but also need to reproduce there successful potential range of the species is larger than its actual range aka the species could live in certain areas where it currently does not If behavior does not limit the distribution biotic? abiotic?

Chapter 53--- Population Ecology Population Ecology explores how biotic and abiotic factors influence the density, distribution, size, and age structure of populations Population- a group of individuals (aka subset of a species) of the same species occupying a given area o Rely on same resources, influenced by similar environmental factors, and likely to interact and breed with one another o POPULATIONS CAN EVOLVE NOT SPECIES OR INDIVIDUALS Density and Dispersion o Density- the number of individuals per unit are or volume o Dispersion- the pattern of spacing among individuals within the boundaries of the population

o Usually impractical or improbable to count all individuals within a population use sampling techniques to estimate density Patterns of Dispersion Most common pattern of dispersion= clumped Survivorship Curves- a plot of the proportion or number in a cohort still alive at each age o Type 1- Flat at the start, then steep drop Many mammals, including humans, have this curve (few offspring, but lots of care) o Type 2- line with constant slope (straight line)- constant death rate Squirrels, rodents, some lizards, some plants o Type 3- steep drop at beginning (high death rates of the young) then flattens out as death rates decline Organisms with large # of offspring but little care (fish)

Elephant- Type 1, Bird- Type 2, Insect- Type 3 Reproductiono Semelparity (big-bang reproduction)- reproduce all at one time (salmon) Favored when the survival rate is low

o Iteroparity- (repeated reproduction)- from a certain maturity, produce annually/repeatedly (lizards) Favored in a more dependable environment where competition may be intense ***trade-off between reproduction and survival Changes in Population Sizes o Birth and Death o Immigration and Emigration Per Capita Rate of Increaseo Change in population size during time interval = (births during time interval +immigrants entering during time interval) (deaths during time interval + emigrants leaving during time interval) Abbreviated (dropping the immigration/emigration N/t= bN dN b= per capita birth rate o (#birth/per time interval) total number present d= per capita death rate N= population size t=time per capita rate of increase r=bd o r > 0 = population is growing o r < 0 = population is declining Simplified: N/t= rN Zero Population Growth (ZPG) occurs when the per capita birth and death rates are equal (doesnt mean there are no births and death, just means they are equal)

Biotic Potential ( rmax or intrinsic rate of increase) maximum rate of increase per individual under ideal conditions

Exponential Population Growth (aka geometric population growth)-growth of a population in an ideal, unlimited environment, represented by a J-shaped curve when population size is plotted over time (max rate of increase is constant) o dN = rmaxN dt o Assumes that resources are unlimited (not realistic) Carrying capacity (K)- the maximum population size that can be supported by the available resources o Limiting Factors- lead a population growth towards K, an essential resource in short supply Logistic Population Growth- population growth that levels off as population size approaches carrying capacity, S-shaped curve o dN =rmax N (K-N) dt K

Overshooting Capacity-

K-selection- selection for life history traits that are sensitive to population density (density-dependent selection) o Operate in a population living at a density near the carrying capacity where competition among individuals is relatively strong Stable Limited by carrying capacity Organisms- larger, long-lived, fewer offspring w/ more care

R-selection- selection for life history traits that maximize reproductive success in uncrowded environments (density-independent selection) o Maximizes r and occurs in environments in which population density is well below carrying capacity or individuals face little competition (often found in disturbed habitats) Unstable Limited by reproductive rate (r) Organisms- smaller, short-lived, lots of offspring with little/no care

Density-Dependent-varies according to density o Competition for resources o Territoriality- competition for space

Disease-depends on certain level of crowding Predation Toxic wastes (by-products) Intrinsic (physiological) factors Aggressive interactions, stress sex-related issues, increased mortality due to crowding Density-Independent- does not vary due to density o Catastrophes o Natural disasters o Diseases- that act at ANY population size Population Dynamics- focuses on the complex interaction between biotic and abiotic factors that cause variation in the size of the population Human Population o 6.6 billion people o Increasing by 75 million a year (1.26%) o Demographic transition= Zero population growth= low birth rate-low death rate Key is reduced family size o Age-structure pyramids Rapid growth= bottom heavy triangle (Afghanistan) Slow growth= relatively even (US) No growth= top heavy (Italy) ***Not only predicts a populations growth trends but also illuminates social conditions o Ecological footprint- the aggrefate land and water are required by a person, city or nation to produce all of the resources it consumes and to absorb all of the waste it generates (used to estimate the worlds carrying capacity) o Todays Environmental Problems Habitat Loss Invasive Species Populations Growth Pollution Overuse of resources Chapter 22-24 Keystone species- when removed from habitat, many other organisms die off Species Richness- how many species Diversity- how many of each species Two principles lie at the core of the science of evolution o Common descent w/ modifications o Natural selection It maintains favorable genotypes in a population Shapes evolution, not design Scientists o o o o

o Alfred Russel Wallace- developed a natural selection hypothesis similar to Darwin, but admired/thought Darwin had developed the idea so extensively, he let Darwin be the main architect o Charles Lyell (1830)- earth is changing (uniform rate of change, same things happening now were happening millions of years ago) o JB de Lemarch (1809)- species change due to inheritance of acquired characteristics, modifications passed to offspring o George Cuvier (1769-1832)- fossils, developed paleontology o Darwin- Decent with Modification Evidence for Evolution- lines of evidence internally consistent and consistent with each other o Fossils o Comparative anatomy/ homologous structures o Direct Observation o Biogeography- geographic distribution of the species o Molecular- genetic code Evolutionary Fitness- number of offspring left behind Herbert Spenser- survival of the fittest Artificial selection- when human being choose organisms with specific characteristics (stock), humans are performing the role of the environment Hardy and Weinberg Equilibrium Principle: We have gone from allele frequencies in the parental gene pool to genotype frequencies among the offspring o p+q=1 o p2 + 2pq + q2 = 1 Assumptions: No migration No mutations No chance events No natural selection No non-random mating Evolution takes place when the allele frequency in a population changes o 5 agents of microevolution Mutations: <30,000 genes Gene flow- immigration and emigration Genetic drift- chance events Cause allele frequency to fluctuate unpredictably especially in small populations (smaller population the bigger effect random chance has (coin-flip) Bottleneck effect- natural disaster causes reduced gene pool Founder effect- very low genetic variability because the first one to a place reduces genetic variation to almost Non random mating-

Natural selection- maintains favorable traits in a population and accumulates them If enough variation exists in a species and its environmental conditions change evolution Three modes of selectiono Directional selectionso Disruptive selectionso Stabilizing selectionsWe can measure evolution by the different allele frequency from one generation to the next (Hardy-Wein) evolution Biological Species Concept- Erust Meyer o Groups of individuals (species) that potentially/actually can interbreed with each other and have viable and fertile offspring Shortcomings Some species are asexual- bacteria Fossil species Morphological species concept- structure size anatomy Paleontological species concept- fossil species with distinct morphological characteristics Ecological species concept- in terms of their ecological niche Phylogenetic species concept- according to its genetic history Discrete vs. Quantitative o Discrete- either/or (plant can be either white or orangedepends on one genes) o Quantitative- depends on more than one gene (lots of options) Speciation can take place with or without geographic separation o Allopatric- different land Evidence- genetic variation within a population o Sympatric- same land Associated with character displacement Adaptive Radiations- periods of evolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological roles/niches

CHAPTER 26: Phylogeny and the Tree of Life Phylogeny- the evolutionary history of an organism o Cladistics- study of resemblances among clades o Clade- having all descendants that belong to one ancestor Monophyletic- one ancestral species and ALL its descendants Paraphyletic- one ancestral species and SOME of its descendants Polyphyletic- taxa with DIFFERENT ancestors

Taxonomy- the naming and classification of organisms o 1758- Carolus Limaeus- binomial nomenclature King Phillip Came Over For Great Sex Kingdom Phylum Class Order Family Genus Species Analogy vs. Homologyo Analogy-due to convergent evolution (red herring because look like similar ancestor) o Homology- common ancestor Convergent Evolution- occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms with different evolutionary lineages. Shared derived characteristic- an evolutionary novelty unique to a particular clade (their ancestors did not have them) Maximum parsimony- investigate the simplest explanation that is consistent with the facts Maximum likelihood- given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events Orthologous genes- homologous genes that are found in different species because of speciation (can only diverge after speciation) Paralogous genes- result from gene duplication so they are found in more than one copy in the same genome Molecular clock- a yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates o Assumption it that the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the species branched from their common ancestor (divergence time) Neutral Theory- much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection. Monera- one of the five kingdoms in the late 1960s but not accepted anymore because as it included all prokaryotes, it is now widely understood based ib genetic data the diversity within the Monera (Bacteria and Archaea, aka members in two different domains) Prostista- also a kingdom that is not recognized because it is polyphyletic (aka members that are closer to plants, fungi, or animals) Three Domain System o Bacteria o Archaea

o Eukarya

Horizontal gene transfer- a process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infections, and perhaps fusions of organisms o First eukaryote result from the fusion of an ancestral bacterium and an ancestral archaean? (endosymbiosis) Chapter 27-Bacteria and Archaea: Prokaryotes are the most abundant organism on Earth- collective biological mass is at least ten times that of all eukaryotes o One of the reasons this is true is due to their ability to adapt to a broad range of habitats (masters of every environment) Prokaryotes are though to be the first organisms to inhabit the Eath Attributes o Unicellular (exception if when some aggregate temporarily or permanently in colonies) o Small- diameter= .5-5m (smaller than the 10-100 m eukaryotic) o Variety of shapes Cocci- sphere Bacilli- rods Spirochete- spiral o Reproduce asexually (binary fission) with short generation time Because of this they have the ability to adapt rapidly 5/7/12 5/7/12Sto new conditions o No membrane bound organelles o High genetic variation o Significantly less DNA (nucleoid rather than nucleus) o Cell wall made of________ covered by a capsule, a sticky layer of polysaccharide or protein (this enables the organisms to adhere, some also use fimbriae which are hairlike protein appendages to adhere) Bacteria- peptidoglycan Archaea- no peptidoglycan, but polysacchrides and proteins o Mobility of Eukaryotes- most common method is flagella, exhibit taxis

o Endospores- a thick-coated, resistant cell produced by a bacterial cell exposed to harsh conditions, created when an essential nutrient is lacking copies its chromosome and surrounds it with a tough wall, dehydrates and remains dormant till environment improves then rehydrates and is viable. Combination of DNA results from o Transformation- the genotype and possibly phenotype of a prokaryotic cell are altered by the uptake of foreign DNA from its surroundings o Transduction- bacteriophages (viruses that infect bacteria) carry bacterial genes from one host cell to another This is a type of horizontal gene transfer o Conjugation- genetic material is transferred between two bacterial cells that are temporarily joined F factor- consists of about 25 genes which is necessary to form sex pili and donate DNA Mode of Nutrition Energy Source Carbon Source Photoautotroph Light CO2 Chemoautotroph Inorganic chemicals CO2 Photoheterotroph Light Organic Compounds Chemoheterotroph Organic compounds Organic Compounds Nitrogen fixation- converting atmospheric nitrogen (N2) to ammonia (NH3) o Cyanobacteria and some methanogens o Heterocytes- specialized cells that carry out only nitrogen fixation Archaea: Characteristics o Prokaryotic o Ribosomal DNA similar to eukaryotic histones (proteins in which DNA can wind) associated with DNA o Not affected by antibiotics o Cell wall without peptidoplycan (protein, glycoprotein, and/or polysaccharides) o Membrane is different and chemically unique Lipids are ether-linked and branched hydrocarbons and rings (not fatty acids) Glycerol can be attached to both ends of lipid molecule (diglycerol) Biotopeso Methanogens- strictly anaerobic o Halophiles- need lots of salt, brightly colored o Hyperthermophiles- mostly aerobic o Thermoacidophiles- no cell wall Extremophiles- the first prokaryotes assigned to this domain who live in environments so extreme that few other organisms can survive there

Bacteria: split into two different groups: o

o Extreme halophiles- halo=salt- live in highly saline environments o Extreme thermophiles- thrive in very hot environments Methanogens- live in more moderate environments- use CO2 to oxidize H2 and release methane as waste product o Decomposers that are posisoned by oxygen (anaerobes) o Most widely distributed o 4H2 + CO2 CH4 + 2H2O

o o Gram Positive- purple o Gram Negative- pink lipid portion of the lipopolysaccharides are toxic causing fever and shock more resistant to antibiotics than gram-positive due to their outer membrane Proteobacteria- large, diverse clade of gram-negative bacteria that includes photoautotrophs, chemoautotrophs, and heterotrophs. o Includes photosynthetic sulfur bacteria o Mitochondria relatives (alpha proteobacterium) o Pathogens- salmonelle and vibrio cholerae Cyanobacteria- relatives of chloroplasts (3.5 mya photosynthesis produces oxygen) Shapes o Cocci- sphere o Bacilli- rods o Spirochete- spiral mobile, parasitic pathogens (lyme disease, syphilis) Prokaryotes play a huge role in the chemical recycling of elements between the living and non-living components of the environment. Often form symbiotic relationships with much larger organisms Pathogens- parasites that cause disease

o All pathogenic prokaryotes known to date are bacteria that cause illness in humans Exotoxins- proteins secreted by certain bacteria and other organisms Endotoxins- lipopolysaccharide components of the outer membrane of gram-negative bacteria (released only when the bacteria dies and their walls break down) Bioremediation- the use of organisms to remove pollutants from soil, air, or water Comparison:

CHAPTER 28: Protists: o Protist- an informal term applid to any eukaryote that is not plant, animal, or fungi. Most are unicellular though some are colonial or multicellular o Protista= polyphyletic- some protists more closely related to plants, fungi, or animals than other protists o Ingestive- (animal-like) protozoa o Absorptive- (fungus-like)

o o

o Photosynthetic- (plant-like) alga Characteristicso Have a nucleus and other membrane bound organelles o Most unicellular o Some reproduce asexual, some sexual Mixotroph- combine photosynthesis and heterotrophic nutrition Protist diversity due to endosymbiosis o Secondary endosymbiosis- a process in eukaryotic evolution in which a heterotrophic eukaryotic cell engulfed a photosynthetic eukaryotic cell, which survived in a symbiotic relationship in the heterotrophic cell Every child rides a unicorn: o o

o Excavata Euglenozoans Kinetoplastids- have a single, large mitochondrion that contrains an organized mass of DNA called a kinetoplast (sleeping sickness) Euglena- mixotrophs with flagella Diplomonads and Parabasalids (vaginitis). Modified mitochondria (does not have DNA) o Diplomads- mitosomes o Parabasalids- hydrogenosomes Adapted to anaerobic environments

o Glycolysis Lack plastids o Chromalveolata- includes Plasmodium which causes malaria Alveolates Dinoflagellates (phytoplankton)-red tide Ciliates- paramecium Plasmodium- malaria S o o o o o o o o o o o o o o

Stramenopila- diatoms-marine alga Oomycetes- water molds- not related to fungi (convergent evolution) o Rhizaria- monophyletic-amoebas with pseudopods o Archaeplastida- monophyletic-descended from ancient protist who engulfed cyanobacterium- photosynthetic species like red and green alga o Unikonta- includes fungi and animals, also slime molds

o Alteration of generations-applies only to life cycles in which both haploid and diploid stages are multicellular

o Heteromorphic- the sporophyte and gametophyte are structurally different o Isomorphic- the sporophyte3 and gametophyte look similar to each other but differ in chromosome number

CHAPTER 29. 30, 35, 31, 38, 36, 37, : PLANTAE o Closest relative to land plants is green alga (protist) called charophtyes o Characteristics: o Multicellular o Eukaryotic o Photosynthetic autotrophs o Cell walls of cellulose o Chloroplasts with chlorophylls a and b o Distinguish plants= vascular vs. non vascular plants o Vascular tissues- cells joined into tubes that transport water and nutrients throughout the plant body o Bryophytes-non vascular plants- not monophyletic- clade- alteration of generations- life cycles dominated by gametophytes (held down by rhizoids)- sexual and asexual reproduction- bryophyte sporophytes cannot live independently (foot, seta (stalk), capsule) Hepatophyta- liverworts Anthocerophyta- hornworts Bryophyta- mosses o Vascular Plants- 93% of all plants (420 mya) Seedless (paraphyletic)-grade Lycophytes- club mosses and their relatives o Dominated by gametophyte Pterophytes- ferns and their relatives o More closely related to seed plants and have megaphyll leaves, overtopping growth, and roots o Dominated by sporophyte Seed (360 mya) Reduced gametophytes (microscopic) Heterospory- megasporangia produce megaspores that five rise to female gametophytes (in an ovule) whereas microsporangia produce microspores that give rise to male gametophytes (in a pollen grain) Integument- (forms the seed coat) layer of sporophyte tissue that contributes to the structure of an ovule of a seed plant (ovule= megasporangium, megaspore, and their integuments) o Gymnosperms- naked seeds-their seeds are not enclosed in chambers- one integument Thick cuticles and small surface area because of needle shaped leaves Cycadophyta- 2nd largest group Ginkgophyta- gingko biloba is the only surviving species Gnetophyta

Coniferophyta- largest gymnosperm phylum- most are evergreens, large trees, 600 species o Angiosperms-flowering plants- 90% of living plants- two integuments o Vascular Plants o Transport Xylem- water and minerals Tracheids- tube-shaped cells that carry water and minerals up from roots (lignified) o Since non vascular plants dont have theses, sometimes vascular plants are called tracheophytes Phloem- distributes sugars, aino acids, and other organic products o Leaves Microphylls vs. megaphylls Microphylls- only lycophytes have them- small, spineshaped leaves Macrophylls- highly branched vascular system, support greater photosynthetic productivity Sporophylls- modified leaves that bear sporangia o CellsTissueOrgans o Tissue- a group of cells with a common function, structure, or both o Organ- consists of several types of tissue that carry out a particular function o Plant Structure and Development o Plants with 3 basic organs- roots, stems, and leaves (forming a root and shoot system) Roots Taproot system- eudicots and gymnosperms o One main vertical root (taproot) gives rise to lateral roots (branch roots) Fibrous root system- a mat of generally thin roots spread out below the soil system with no main root (shallow penetration) Stem- organ consisting of an alternating system of nodes (points at where leaves are attached) and internodes (the stem segments between nodes) Axillary bud- a structure that has the potential to form a lateral shoot (branch). The bud appears in the angle formed between a leave and a stem Apical bud- a bud at the tip of a plant stem (terminal bud)

o Apical dominance- the inhibition of axillary buds by an apical bud (proximity) Leaves- main photosynthetic organ (green stems also perform) Consists of flattened blade and a stalk (petiole) which join the leaf to the stem at a node Veinso Monocots have parallel major veins o Eudicots- have branched network of veins o Plant Tissue Three tissues: Dermal- plants outer protective covering o Non-woody plant- epidermis Cuticle- waxy coating on the epidermal surface protects from water loss o Woody- periderm Vascular- long-distance transport of materials between the root and the shoot system (stele- vascular tissue of root/stem) o Xylem- water/minerals o Phloem- sugar (product of photosythesis) Groundo Internal to vascular system- pith o External to vascular system- cortex Meristems- perpetually embryonic tissues Apical- at the tips of roots and shoots and in the axillary buds of shoots (primary growth) Lateral- growth in the girth of the plant, thickness of stem and roots (secondary growth) ---all gymnosperms and many euidcots (rare in mnocots) o Vascular cambium- adds layer of vascular tissues (xylem and phloem) o Cork cambium- replaces the epidermis with periderm o Plant Cells Parenchyma- perform most of the metabolic function of the plant (including photosynthesis), thin-walled and many-sided, most abundant and versatile Collenchyma-supporting cells, form veins of leaves, cellulose and pectin Sclerenchyma- support the body of the plant (lignin), coat the seeds and form a sheath around the vascular tissues Xylem- cells are called vessels and tracheids and are dead at maturity, form pipelines

Phloem- cells called sieve-tube members are alive at maturity, interconnect through perforations the ends or tiny pores in the sides of the walls o Indeterminate growth- plant consists of embryonic, developing, mature organs o Life cycles of Plants o Annuals- complete their life cycle in a single year or less o Biennuals- complete their life cycle in two years (two growing seasons) o Perennials- live many years

o Bark- secondary phloem + periderm (everything external of the vascular cambium Angiospermso Sporophyte is the dominant generation o Floral organs (Complete flowers have all four basic floral organs) o Sepals- enclose and protect the floral bud before it opens, green and more leaflike in appearance o Petals- brightly colored and advertise the flower to insects/pollinators o Stamens-

Filament- stalk Anther- terminal structure in which the microsporangia produce pollen Contains 4 microsporangia o In the microsporgania- diploid cells called microsporocytes which each undergo meiosis producing four haploid microspores which undergoes mitosis giving rise to a haploid male gametophyte consisting of two cells Generative cell- divides by mitosis and forms two sperm cells One sperm fertilizes egg, other combines with the two polar nuclei forming a triploid nucleus (endosperm) Tube cell- produces the pollen tube o Carpels/Pistil Ovary- which contains the ovule, at the base of the style Opening in the ovule for sperm = micropyle First mitotic division of the zygote splits the fertilized egg into a basal cell and a terminal cell o Terminal cell eventually gives rise to most of the embryo o Basal cell continues to divide producing a thread of cells called the suspensor (anchors embryo to parent) Suspensor helps transferring nutrients Style- long, slender neck of the plant Stigma- serves as a landing platform for pollen o Receptacleo o CHAPTER 31: FUNGI o Essential to the well being of terrestrial ecosystem because they break down organic material and recycle the nutrients ---decomposers-parasitesmutualists o Characteristics: o Dominated by the haploid stage o Heterotrophs- cannot make their own food o Eats through absorption of nutrients from the environment outside its body Some accomplish this by secreting powerful hydrolytic enzymes into their surroundings

 Some use enzymes to penetrate the walls of plant cells o Multicellular filaments and single cells (yeasts) Some grow as both filaments and yeasts, even more grow as just filaments, and few grow as just yeasts Yeasts often inhabit moist environments o Hyphae- tiny filaments that form a network to create the body of the fungi Divided into cells by crosswalls (septa) Fungi that lack septa (coenocytic fungi)- continuous cytoplasmic mass having hundreds or thousands of nuclei o Cell walls strengthened by chitin (not cellulose like in plants) o Mycelium- densely branch network of hyphae that infiltrates the material on which the fungus feeds o Haustoria- specialized hyphae that allows fungi to extract nutrients from-or exchange nutrients with- their hosts o Mycorrihizae- mutually beneficial relationships between fungi and plant roots o Ectomycorrhizal- form sheaths of hyphae over the surface of a root and also the extra space of the root cortex o Arbuscular- hyphae through root cell wall and into tubes formed by invagination o Reproduction o propagate by producing a vast number of spores (either asexual/sexual) o nuclei of fungal hyphae and spores of most fungal species are haploid o nuclear envelope does NOT break down o no centrioles, but there are spindle fibers o heterokaryon- mycelium that contains two or more haploid nuclei per cell- genetic material is different across nuclei o homokaryon- no genetic difference o dikaryotic- fungal mycelium with two haploid nuclei per cell (one from each parent o deuteromycetes- fungi with no sexual stage

o o Fungi and Animalia are more closely related than either is to plants or most other eukaryotes o Funginucleariids o Animalschoanoflagellates o Phylum Chytridiomycotao Flagellated zoospores o Earliest fungi group o Decomposers, parasites o Responsible for major decline in amphibians o Phylum Zygomyceteso Grow in bread and other food (fast growing) o Resistant zygosporangium as sexual stage o Phylum Glomeromyceteso Many form relationships with plants Arbuscular mycorrizae o Phylum Ascomyceteso Sac fungi- production of sexual spores in saclike asci o Fruiting body= ascocarp o Asexual spores- conidia o Phylum Basidiomyceteso Club fungi- fruiting body= mushroom o Elaborate fruiting body (basidiocarp) containing many basidia that produce sexual spores (basidiospores) o Long lived dikaryotic mycelium o 30% of known species are pathogenslichen-photosynthetic organism and a fungi CHAPTER 32: choanoflagellates o Animal Diversity o Animals are multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers (most are invertebrates) o Reproduce sexually, o Dominated by the diploid stage

o Most are motile, although some are sessile for at least a portion of their lives o Nutrition Plants- autotrophic eukaryotes capable of generating organic molecules through photosynthesis Fungi- heterotrophs that grow on or near their food and feed by absorption Animals- canNOT construct their own organic molecules or feed by absorption, rather they ingest and use enzymes. o Cell Structure Animals are eukaryotes and multicellular No cell walls- cells are held together by extracullular matrix Two types of specialized cells that are not seen in other multicellular organisms: Muscle cells-movement Nerve cells-conducting impulses o Reproduction and Development Diploid stage dominates the life cycle Hox genes- developmental control genes Homologous hox genes establish body plans in animals that have not shared a common ancestor in hundreds of millions of years o

o choanoflagellates ancestor- common ancestor of all living animals o Neoproterozoic Era- (1 Billion- 542 mya)- Ediacaran biota o Paleozoic Era- (542-251mya)-Cambrian explosion- animal diversication. Why? New predator-prey relationships O2 increased dramatically increased metabolic output Evolution of Hox genes o Mesozoic Era- (251-65.5mya) Coral reefs appeared and dinosaurs o Cenozoic Era- (65.5 mya-present) Mass extinction of both terrestrial and marine animals o Body Plan- a set of morphological and developmental traists, integrated into a functional whole-the living animal o Symmetry Radial (usually sessile or slow moving) Bilateral (move more actively from place to place) Dorsal (top) vs. Ventral (bottom) Anterior (front) vs. Posterior (back) o Cephalization- concentrated sensory equipment in the anterior o Tissues Sponges lack true tissue Ectoderm- germ layer covering the surface of the embryo gives rise to the outer covering of the animal Endoderm- innermost germ layer, lines the digestive tube and gives rise to the digestive track Mesoderm- forms the muscles and other organs between the digestive track and outer covering Diploblastic- has only endo/ectoderm- cnidarians and comb jellies Triploblastic- has all three germ layers- animals with bilateral symmetry o Body Cavity- Coelom Most triploblastic animals possess body cavity (air/fluid-filled) that separates the digestive track from the outer body wall Coelomates (derived mesoderm), Pseudocoelomates (mesoderm and endoderm), Acoelomates (lack body cavity) Only 3 phyla lack a coelom o Cnidaria o Platyhelminthes o Porifera Coelomates is a grade not a clade

o Morphological and Molecular Agreements o All animals share a common ancestor (monophyletic kingdom) o Sponges are basal animals o Eumetazoa- clade of animals with true tissues o Most animal phyla belong to the clade Bilateria o Chordates and some other phyla belong to the clade Deuterostomia o Three clades of bilaterally symmetrical animals: o Deuterostomiao Lophotrochozoa- refers to two different features Lophophore- a crown of ciliated tentacles that functions in feeding Trochophore larva-apical tuft of cilia on top o Ecdysozoa- these animals secrete external skeletons (exoskeletons) and shed them (ecdysis)

Chapter 33- Invertebrates: o Invertebrates- animals that lack a backbone (account for 95% of all known animal species) o Protostomes vs. deutrostomes o Deuterostomia is defined primarily by DNA similarities not developmental similarities o Phylum Porifera (paraphyletic -now Calcarea and Silicea) o Sponges- sessile, suspension feeders, in through spongocoel (pores) out through osculum, lack true tissue Choanocytes- collar cells o Phylum Cnidaria o Jellyfish, polyp, sea anenome, hydras, corals o Diploblastic, radial body plan o Two life stages: Polyp- sessile Medua- motile o Cnidocytes Cnidae- capsule-like organelles that are capable of exploding outward NematocystsLophotrochozoans o Phylum Platyhelminthes o Flatworm, free-living or parasitic, acoelomates o Pharynx o Ganglia- many nerve cells clumped together o Ventral nervous system o Four Classes (Turbellaria (free-living), Monogenea, Trematoda, Cestoda) Trematoda Trematodes or flukes (parasitic) Require an intermediate host in which larvae develop Cestoda Tapeworms- parasitic Scolex-anterior end is armed with suckers and hooks No digestive system, absorption of nutrients through the body surface o Phylum Rotifera o Alimentary cavity-digestive tract- separate mouth and anus o Pseudocoelem filled of fluid giving a hydrostatic skeleton o Parthenogenis- females produce more females from unfertilized eggs o Phylum Ectoproctso Lophophorates o U-shaped alimentary canal o True coelom o Sessile

o Colonial animals that resembles moss o exoskeleton o marine o Phylum Brachiopodso Lamp shells o Lophophorates o U- shaped alimentay canal o True coelem o Sessile o Marine o Phylum Mollusca o Snails and slugs, oysters and clams, octopuses and squid. o Soft bodied animals but secrete hard shell composed of calcium carbonate o Three part body plan Foot (used for movement) Visceral mass (containing most of the internal organs) Mantle (a fold of tissue that drapes over the visceral mass and secretes a shell Mantle cavity- houses fills, anus and excretory pores o Feed using a straplike, rasping organ called radula to scrape up food o Classes: Gastropoda Snails and slugs of mollusks torsion- visceral mass rotates up to 180 degrees open circulatory system Bivalvia Clams, oysters and other bivalves Radula is lost Powerful adductor muscles draw the two halfs close together Suspension feeders Open circulatory system Cephalopoda Octopus, squid, cuttlefishes and chambered nautiluses Active predators Closed circulatory system Sense organs and complex brain o Phylum Annelida o Segmented worms (earth worms-Oligochaeata) Internal and external segmentation o Coelomates o Mostly freshwater or marine o Primitive brain

Ecdysozoans o Phylum Nematoda o Roundworms o Alimentary canal but lack a circulatory system o Phylum Arthropods o Body plan- segmented bodies, hard exoskeleton, and jointed appendages o Open circulatory system- fluid blood= hemolymph Subphylum: Cheliceriforms (sea spiders, horseshoe crabs, scorpions, ticks, mites, and spiders) o Chelicerae-clawlike feeding appendages (pincers + fangs) o Anterior= cephalothorax and posterior=abdomen o Arachnids-scorpions, spiders, ticks and mites Pedipalps- found in arachnids used in sensing, feeding, and reproduction Spiders= book lung Myriapods (centipedes and millipedes) o diplopoda- millipedes o chilopoda- centipedes- carnivorous-poisonous Hexapods (insects and their wingless, six-legged relatives) o More species-rich than all other forms of life combined o Incomplete metamorphosis- young reesemble the adult form o Complete metamorphosis- larval stage looks entirely different than adult stage Crustaceans- (crabs, lobsters, shrimps, barnacles and others) o Isopod-pill bug o Decapod-lobsters crayfish crab and shrimp o Copepods- planktonic crustaceans and shrimplike krill Deutrostomia o Echinodermata o Sea star, sea urchins, etc o deuterostome o slow moving or sessile marine animals o water vascular system-hydraulic canals branching into tube feet o sexual reproduction includes the gametes being released into water (separate male and female) o adult= not truly radial symmetry, larva=bilateral

o Classes: Asteroida sea stars Echinoidea- sea urchins and sand dollars

CHAPTER 34: CHORDATA Protostome: Blastopore=mouth, spiral cleavage, determinate cell division, coelom from split in mesoderm Deuterostomes: Blastopore= anus, radial cleavage, indeterminate cell division, coelom from outpocketing Made up of phylum like Chordates and Echinoderm o Phylum: Chordates

Bilateral symmetry

Synamorphies (shared derived characteristics) of chordates:

CHORDATES: notochord, dorsal/hollow nerve cord, pharyngeal slits, post anal

tail o o o Cephalochordata-lancelets- basal chordates, exhibit 4 derived characteristics, invertebrates, marine suspension feeders Urochordata- tunicates- marine suspension feeders, larvae display 4 derived characteristics, 9 Hox genes instead of 13 Hox genes CRANIATES-appearance of a head, two Hox gene clusters, neural cresta collection of cells that give rise to features like teeth, bone, and skin, have a heart with at least 2 chambers, red blood cells w/ hemoglobin Myxini- hagfishes- jawless, marine, cephalization (head w/skull of cartilage, brain, eyes, sensory organs) VERTEBRATES: backbone of vertebrae (segmented backbone), Dlx genes duplication, more complex nervous system Petromyzontida- lampreys- jawless vertebrates, attach to fish and suck blood, no jaws, no paired appendages GNATHOSTOMES: hinged jaw, four Hox gene clusters, paired appendages, enlarged forebrain o Chondrichtheys- sharks, rays, chimaeras- cartilaginous skeleton, DIFFERENT than Osteichthyans because ossified endoskeleton o OSTEICHTHYANS: bony skeleton Actinopterygii- ray-finned fishes- bony skeleton, maneuverable fins supported by rays, SWIM BLADDER LOBE-FINS: muscular fins or limbs Actinistia- coelacanths- ancient lineage of aquatic lobe-fins, living fossils, 1938: Latimeria Dipnoi- lungfishes- freshwater lobefins with both lungs/gills, Chytrid fungi leads to decline of amphibians

TETRAPODS: four limbs, neck,

fused pelvic girdle, pharyngeal clefts give rise to parts of the ear, certan glands and other structures o Amphibia- frogs, salamanders4 limbs, skin functions in gas exchange, live in water and on land o AMNIOTES: amniotic egg, rib-cage ventilation, water impermeable skin Reptilia- turtles, snakes, crocodiles, birds- amniotic egg, rib cage ventilation, exothermic except birds, scales(hydrate) Mammalia-hair and mammary glands-milk, diaphram ventilation, belong to synapsidssingle temporal fenestra, Jurassic

o Oviparous- reproducing external fertilization o Ovoviviparous- internal fertilization- retain fertilized eggs in oviduct

o o Amniotic Egg Amnion- encloses a compartment of fluid that bathes the embryo and acts as a hydraulic shock absorber Shell- slows dehydration of the egg Chorion- gas exchange Allantois- gas exchange, waste Yolk Sac- nutrition

o Reptile clade includes birds because o Birds developed from the Archaeopteryx Significant because showed the link between birds and dinosaurs/reptiles, feathered wings but retained ancestral dinosaur characteristics such as teeth, clawed digits, and a long tail o Mammals Monotremes Platypuses and 4 species of spiny anteaters, lay eggs, lack nipples, baby sucks milk from mothers fur, lower metabolic rate than marsupials and eutherians Marsupials Opossums, kangaroos, and koalas Give birth to live young, just born extremely early and completes ins embryonic development while nursing in a meternal pouch (marsupium) Eutherians Placental mammals More complex placentas than marsupials o Primates Tarsiers, monkeys, and apes Humans belong to the ape group Large brain (forebrain more prominent), short jaw, opposable thumb, forward directed vision o Humans Large brain Bipedal locomotion Stand upright Capable of language, symbolic thought, manufacture/use of complex tools Reduced jawbones and jaw muscles with a shorter digestive tract Hominin- a species on the human branch of the evolutionary tree (ex. Homo sapiens) Evolution of Humans o Australopith- Lucy Different than Homo sapiens: Small brained Long jaw Long arms for swinging in trees Similarities: Bipedal o Evolution of Homo Homo habilis- Tools + Brain

Homo ergaster- Tools + Brain + Less Tree Adaptations Sexual dimorphism- males and females became closer in size Homo neanderthalensis- not part of the evolution of humans (big debate) o Evolution of Human Traits Bipedal (climate became drierless trees evolution favored walking instead of swinging) Tool use Bigger Brains Reduced sexual dimorphism FOXP2 gene (language) Art FOXP2 thought to play a role in human language. Also isolated in a variety of mammals including mice, chimps, and orangutans

CHAPTER 41: Animal Nutrition Vitamins- organic molecules with diverse functions that are required in the diet in very small amounts o Vitamin-B3 (Niacin) deficiency was affecting share croppers, known as the disease Pellagre. Joseph Goldberger discovered the reason behind it (the deficiency) in 1914 Food Processing (Carbs, lipids and proteins are digested differently!) o Ingestion Eating food o Digestion Food is broken down into molecules small enough for body to absorb o Absorption Cells take up small molecules o Elimination Undigested material passes out of the system Enzymatic hydrolysis- the process in digestion that splits macromolecules from food by enzymatic addition of water o Most occurs in the small intestines Intracellular vs. extracellular digestion o Intracellular- food vacuoles- occurs after cell engulfs solid food (phagocytosis) or liquid food (pinocytosis), these newly formed vacuoles fuse with lysosomes which deliver the enzymes to break down this food within its compartment. o Extracellular- break down of food in compartments that are continuous with the outside of the animals body. Alimentary canal-complete digestive track- digestive tube extending between the mouth and anus

Peristalsis- alternating waves of contractions and relaxations in the smooth muscles lining the canal that pushes food along Sphincter- regulate the passage of material between compartments The Path of Food o Enters the mouth (oral cavity) and mechanical digestion begins as teeth grind food (increasing surface area) o Nervous reflex is stimulated which causes the salivary glands to deliver saliva (chemical digestion-amylase) o Food (bolus) is pushed to the back of the oral cavity and into the pharynx (throat region) and down the esophagus which leads to the stomach Epiglottis prevents food from going down the trachea (the other passage way of the pharynx) o Stomach is located below the diaphragm in the upper abdominal cavity and its main function is to store food and continue digestion. Stomach releases gastric juice and mixes it with a churning action (creating chyme) 10% of absorption of nutrients Highly folded (rugae), dotted with pits leading to tubular gastric glands Two components of gastric juice that carry out chemical digestion: HCL- disrupts extracellular matrix, denatures proteins o Parietal cells Pepsin-breaks peptide bonds o Chief cells o Sphincters help regulate the movement of chyme from the stomach to the small intestines o Small intestines- 3 parts: duodenum, jejunum, and ileum, 80% nutrients are absorbed here Duodenum- first 25 cm of the small intestine, chyme is mixed with digestive juices from the pancreas, liver, and gallbladder as well as the intestinal wall itself. Absorption- most absorption of nutrients occurs in the small intestines, huge surface area (300m2), villi are the sites of absorption (into bloodstream), transport across the epithelial cells can be active/passive (fructose- facilitated diffusion, amino acids, small peptides, vitamins, and glucose- pumped against the concentration gradients by epithelial cells) active transport allows for much more absorption Villi- a finer-like projection of the inner surface of the small intestine Microvilli- one of many fine, finger-like projections of the epithelial cells in the lumen of the small intestine that increase its surface area (brush border)

o Large Intestine- 3 parts: colon, cecum, rectum, 10% nutrients absorbed here T-shaped junction One arm= colonanus o Major function of colon is to recover water (osmosis) o E. coli resides in the colon- creates by-product gases (ex. methane) but also produces vitamins (ex. bacteriavitamin kabsorbed) Rectum-feces are stored until they can be eliminated (2 sphincters- 1 voluntary, 1 involuntary) Eliminated through the anus Other arm- a pouch called cecum- fermenting ingested material o Appendix-finger-like extension of the human cecum has a minor and dispensable role in immunity Carbohydrates, Lipids, and Proteins are Digested Differently o Carbohydrates: First type of macromolecule to be worked on by enzymes in the human digestive system is carbohydrates Digestion of carbs begins in the mouth, 3 major pairs of salivary glands (we produce 1 to 1.5 L of saliva a day) Amylase + maltose Continued digestion in the duodenum by pancreatic enzymes Enzymes attached to the villi in the small intestine complete the carb digestion Amylase and maltase o Lipids: Digestion of lipids begins in the small intestine by bile (bile salts emulsifies fats, produced in liver/stored in gallbladder) Then by pancreatic enzymes (Lipases) Next, unabsorbed lipids are metabolized by bacteria Very little lipid is eliminated in feces Lipid characteristics Storage of energy Glycerol and fatty acids Hydrophobic Insulate axons (myelin sheath) Move in bloodstream as CHOLESTEROL (Typical-170210, Desired <200) o HDL (High-Density Lipoprotein)- Good Typical- 35-85 (mg/dl)

o Proteins: Digestion starts with stomach acids denaturing the proteins and transforming them into strings of amino acids. These amino acids are further broken down by pepsin The next step is pancreatic enzymes breaking the protein fragments into molecules with 1 to 3 amino acids The small intestine then further breaks these chains down into individual amino acids that can be absorbed into the bloodstream through the villi peptidase Fats: o Saturated- MOST DETRIMENTAL TO YOUR HEALTH, solid at room temperature, maximum number of hydrogen bonds o Unsaturated Monounsaturated- lowers bad cholesterol (LDL) but leaves the good (HDL), liquid at room temperature, two hydrogen atoms missing with a double bond between two carbon atoms replacing them (olive oil) Polyunsaturated- lowers both LDL and HDL levels, liquid at room temp, more than 2 hydrogen atoms missing o Trans- raises LDL and lowers HDL levels, contributed to heart disease, formed during hydrogenation (unsaturated fats are bombarded with hydrogen to protect the fat from bacteria or air exposure) does not occur naturally o Omega-3 Fats- polyunsaturated fatty acids, deemed essential fatty acids, lower triglyceride levels, found in flaxseed oil, soybean oil, walnuts, kale, spinach, salad greens, and fatty fish Needed for normal body functions including blood clotting and building cell membranes in the brain Evolutionary Adaptations of Digestive System Correlate with Diet o Dentition (Assortment of Teeth) Carnivores- pointed incisors and canines Herbivores- teeth with broad, ridged surfaces to grind, modified incisors/canines for biting off pieces of vegetation (not shredding/cutting) Ominvores- two incisors for biting, a pointed canine for tearing, two premolars for grinding, three molars for crushing ***fangs are also adaptation of teeth o Alimentary Canal Longer in herbivores and omnivores because vegetation is more difficult to digest 3

Desirable- >60 o LDL (Low-Density Lipoprotein)- Bad Typical: 60-140 mg/dl Desirable- <100

o CHAPTER 44: OSMOREGULATION: hypertonic- fluid in surrounding cell environment have more solutes than that of cytoplasmwater diffuses out of tissues hypotonic- fluids in cytoplasm have more solutes than that of the environment water diffuses into tissues CHAPTER 48: Neurons, Synapses, and Signaling: Neurons- the nerve cells that transfer information within the body Brains- organ of the central nervous system where information is processed and integrated Ganglia- a cluster (function group) of nerve cell bodies in a centralized nervous system Information processingo Sensory input Sensory neurons transmit information from eyes and other sensors that detect external stimuli or internal conditions o Integration Receives information from the sensory neurons and analyze and interpret them, taking into account the immediate context and the animals experience (vast majority of neurons in brain are interneuron, which make only local connections) o Motor output Relies on neurons that extend out of the processing center (brain or ganglia) in bundles called nerves and generate output by triggering muscle or gland activity

Central Nervous System- (CNS)- the neurons that carry out integration are organized in this system which includes the brain and nerve cord o Integration Brain Spinal Cord Peripheral Nervous System (PNS)- the neurons that carry information into and out of the CNS o Sensory Input o Motor Output Cranial Nerves Spinal Nerves Structure and Function of a Neuron

Dendrites- highly branched extensions that RECEIVE signals from other neurons Axon- each neuron has a single axon which is an extension that TRANSMITS signals to other cells (often much longer than dendrites) o Axon hillock is the cone shaped region of an axon where it joins the cell body (region where the signals that travel down the axon are generated) Synapse- the junction where one neuron communicates with another cell across a narrow gap, neurotransmitter molecules released by neuron diffuse across the synapse, relaying messages to other cells Synaptic Terminal- a bulb at the end of an axon in which neurotransmitter molecules are stored and from which they are released Neurotransmitters- a molecule that is released from the synaptic terminal of a neuron at a chemical synapse, diffuses across the synaptic cleft, and binds to the postsynaptic cell, triggering a response Presynaptic cell- transmitting neuron Postsynaptic cell- receiving neuron/cell

Glial cells-glia- supporting cells that are essential for the structural integrity of the nervous system and for the normal functioning of neurons (outnumber neurons in the brain) o Insulate axons of neurons o Nourish neurons o Regulate the extracellular fluid surrounding the neurons Ion Pumps/Channels and Resting Potential o Membrane potential- a voltage (difference in electrical charge) across their plasma membrane In neurons, inputs from other neurons or stimuli cause changes in this membrane potential that act as signals, transmitting and processing information o Resting potential-membrane potential of a resting neuron (one that is not sending signals) Usually between (-60 and -80 mV) Negative sign shows the inside of a neuron at rest is negative relative to the outside o Formation of Resting Potential K+ and Na+ play critical roles in formation of resting potential, however, neither is at equilibrium in a resting neuron Concentration in mammalian neurons: o K+ is 140mM inside cell, 5mM outside o Na+ is 15mM 150mM outside **nearly opposites Sodium-potassium pumps actively transport Na+ out of the cell and K+ into the cell using energy from ATP hydrolysis Ion channels (pores formed by clusters of specialized proteins) allow for ions to diffuse back and forth across the membrane. If any net movement of positive/negative charge voltage occurs Ion channels have selective permeability (potassium channel only allows K+ ions, not Na+) Resting neuron has many open potassium channels, but not a lot of open sodium channels Nerst equation (human body temp 37, ion with net charge of 1) o Eion= 62 mV(log ionoutside/ioninside) o Active Potential When neurons are active membrane permeability and membrane potential change due to the presence of gated ion channels Gated ion channels- open and close in response to a stimuli When gated potassium channels that are closed in a resting neuron are opened, the membranes permeability to K+

increases thereby making the inside of the membrane more negative This creates hyperpolarization (the state where the inside become more negative to the outside) which reduces the change that a neuron will transmit a nerve impulse Depolarization is opposite- reduction in the magnitude of the membrane potential, usually involves sodium channels Many of these gated channels are voltage-gated, meaning they open/close in response to a change in the membrane potential Action potential- a rapid change in the membrane potential of an excitable cell/neuron caused by stimulus-triggered, selective opening and closing of voltage sensitive gates of sodium and potassium ion channels (all-or-none events) Action potential= nerve impulses/signals that carry information along the axon Occur whenever a depolarization increases the membrane voltage to the threshold o Mammalian neurons threshold- -55mV Represent positive feedback once the voltage-gated sodium channels are opened this causes further depolarization Acts as a long-distance signal by regenerating itself as it travels from the cell body to synaptic terminals (this is due to the depolarization of the neighboring regions) Conduction speed at which action potentials are transmitted rely on: Axon diameter-widerfaster o Vertebrate axons have narrow diameters but can still conduct action potentials at high speed due to the adaptation of the myelin sheath Myelin sheath- insulates axons and are produced by two types of glia Mostly lipid, but also water + protein In most cases, action potentials are not transmitted from neurons to other cells. Information is transmitted through synapses o Electrical synapses- gap junctions that allow electrical current to flow directly from one neuron to the other o Chemical synapses- majority of synapses- involve the release of a chemical neurotransmitter by presynaptic neuron from the synaptic vesicles which go across the synaptic cleft and are received by the postsynaptic ligand-gated ion channels

1. Action Potential depolarizes the plasma membrane of the synaptic terminal 2. Voltage-gated calcium channels in the membrane open triggering an influx of Ca2+ 3. Elevated concentration of Ca2+ causes synaptic vesicles to fuse with the presynaptic membrane 4. Vesicles release neurotransmitter into synaptic cleft 5. Neurotransmitter binds to the receptor portion of the ligandgated ion channels in the postsynaptic membrane, opening the channels. 6. Ions can diffuse through the channels (generally creating a postsynaptic potential) a. Excitatory postsynaptic potentials (EPSP)i. Depolarization that brings the membrane to threshold (ex. Na+ and K+ diffuse freely) b. Inhibitory postsynaptic potentials (ISPS) i. Hyperpolarize and move membrane potential farther from threshold (ex. when channels that are selectively permeable for only K+ or Cl-) 7. Neurotransmitter is released from the receptors, and the channels close. 8. Synaptic transmission ends when neurotransmitter diffuses out of the synaptic cleft, is taken up by the synaptic terminal or by another cell, or is degraded by an enzyme Postsynaptic potentials are graded because their magnitude varies due to factors like how many neurotransmitters were released

Postsynaptic potentials also do NOT regenerate and therefore become smaller with distance from the synapse Two EPSP occur at a single synapse in rapid successiontemporal summation add the EPSPs together EPSPs produced by different synapses on the same postsynaptic neuronspatial summation add together o IPSP can counter the effect of a EPSP

CHAPTER 49: Nervous System Nerves- bundles of axons of multiple nerve cells Central Nervous System- brain and spinal cord Peripheral Nervous System- nerves and ganglia Brain and spinal cord o Derived from the dorsal, hollow, embryonic nerve cord Hollow cavity nerve cord transforms into the narrow central canal of the spinal cord and the ventricles of the brain (4) Both the central canal and 4 ventricles are filled with cerebrospinal fluid o Brain/Spinal Cord contain: Grey matter Consists mainly of neuron cell bodies, dendrites, and axons (without the myelin sheath) White matter Consists of bundled axons that have myelin sheaths (giving it a white appearance) Towards outside of the spinal cord, inside of the brain Function is: o linking the CNS to the sensory/motor neurons in the PNS o signaling between neurons of the brain in learning, feeling emotions, processing sensory information, and generating commands Glia in the NS Ependymal- line the venticles and have cilia that promotes circulation of the cerebrospinal fluid Microglia- protects the nervous system from invading microorganisms Oligodendrocytes/Schwann- axon myelination Astrocytes- structural support to neurons and regulate the extracellular concentrations of ions and neurotransmitters Peripheral Nervous Systemo Cranial nerves- connect brain with locations in orans of the head and upper body o Spinal nerves- run between spinal cord and parts of the body below the head

Both contain afferent(receiving) and efferent(transmitting) neurons

Peripheral Nervous System o Somatic/Motor To and from skeletal muscles Voluntary Conscious part o Autonomic Regulates the internal environment Involuntary Unconscious part Divided into sympathetic and parasympathetic systems as well as enteric system

o Parasympathetic- rest and digest- calming and self-maintenance o Sympathetic- fight and flightarousal and energy generation o Enteric- consists of networks of neurons in the digestive track, pancreas, and gall bladder which controls secretion and peristalsis Motor/Somatic and automatic nervous systems often cooperate in maintaining homeostasis Vertebrae Brain: o Brainstem- homeostasis, coordination of movement, conduction of information to and from higher brain centers, responsible for automatic survival functions, oldest part of the brain Consists of: Reticular Formation- nerve

o o o o

network that controls arousal Medulla Oblongata- controls heartbeat and breathing and other homeostatic functions Pons Midbrain-receiving and integrating sensory information Cerebellum- coordinate voluntary movement and balance, helps in learning and remembering motor skills Thalamus- main input center for sensory information going to the cerebrum (brains switchboard), directs messages to specific locations Hypothalamus- control of homeostasis- contains bodys thermostat as well as centers for regulating hunger/thirst/etc Limbic System Hypothalamusmaintenance activities (food/thirst/sex) Hippocampus- memory transfers experiences to long-term Amygdala- linked to emotions Pituitary gland Cerebrum- in humans it accounts for 80% of total brain, divided into right and left cerebral hemispheres-contains cerebral cortex (vital for perception, voluntary movement, and learning)

o Three Brains:

Reptilian-Brainstem and Cerebellum- survival- MORE POWERFUL THAN OTHER TWO BRAINS o Pons- respiratory, facial muscles o Medulla- cough, gag, swallow, vomit o Reticular Formtion- arousal, attention, sleep o Cerebellum- control and coordination of voluntary movements Paelomammalian- limbic system - emotional Neomammalian- neocortical brain- associative reasoning o Conscious thought/logic o Action and planning o Reading writing speaking reasoning o Experience our senses o Awareness o Conscious motor control