OEB 10

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cyanobacteria: only bacterial lineage with oxygenic photosyn, principal primary producers for most of earths history
four important symbioses: micorrhizal in plants, fermentation by microbes and termites in bellies of ruminants, agriculture by humans and other species (ants, beetles, termites), insect pollination of angiospersms
Rubisco: most abundant enzyme, large size with many reaction sites, oxygenase and carboxylase, ****s **** up when reacts with O2, extremely slow due to selectivity of CO2 over O2
informational genes: code for specific features of cell biology - vertically transfered, basic cellular machinery, cells can't function without them so unlikely to move horizontally, useful in constructing phylogenies
symbiosis: living with an unlike partner to mutual benefit, aka controlled parasitisms/mutual exploitation
keystone species: has disproportionate affect on all other species in the community, i.e. a small predator that prevents an herbivore from decimating plant cover, beavers!!!!!!
bottom up: plants determine herbivore abundance, predators/parasites are less important
green revolution 1960-1974: drastic increases in yields with increases in area harvested, increase in the harvest index, introduction of the dwarfing gene to prevent lodging, why the world can sustain such large populations
Why Study prokaryotes: Abudance (most), Distribution (widest range), Diversity (greatest range of metabolic pathways), Evolutionary History (two of three branches), Importance
plasmids: small circular peices of DNA that coding for a single metabolic pathway, multiple copies in a prokaryotic cell, easily shared among prokaryotes adding metabolic functions
What was used to construct the tree of life: DNA sequences of genes that coded for molecules involved with the construction of a subunit of the ribosome
Origin of Complex multicellularity: 500 million years ago
chemolithotrophy: organisms produce ATP during aerobic or anaerobic respiration by oxizing and gaining energy from reduced inorganic compounds
properties of a good electron donor: abundant, non toxic products, high energy (reduced)
quorum sensing: alteration of genetic expression when close to other individuals
double fertilization: 2 sperm nuclei fuse with female gamete, first forms diploid zygote, second combines 1 male nucleus with 2 female to make triploid endosperm, maternal side has more control - allows for selective abortion if needed
Cholorphyll: sits in a specialzed place so that the excited electron can be transferred to the ETC rather than it's natural state, creates fastest biochemical reaction, "bleached" if its electron is not replaced
Horizontal gene transfer: only way for prokaryotes to add info, happens in three ways
Carl Von Linne: invented System Naturae (binomial system for naming species)
example of stable divergence: beak polymorphism based on seed sizes
primary symbionts: obligate for host and bacterium, maternally inherited, reside in very specific/specialized locations, usually nutritional role, strict genomes - little uptake/rearrangement, usu very old, aphids and bacteriocytes that provide tryptophan
transduction: DNA received from donor viruses
Phylogeny: description of the evolutionary relationships among organisms
the great leap forward: behavioral modernity occurred in a sudden event, seems to correlate to the arrival of modern humans, begin burying dead/making clothes/sophisticated hunting techniques/cave painting
explanation for formation of 5 different autotrophic pathways: independent evolution, last common ancestor (selected loss of shared trait), horizontal gene transfer
monophyletic: group contains all and only the descendants of a single ancestor (clades like birds and placental mammals are monophyletic)
groups of extant mammals: monotremes (primitive egg layers in australia) marsupials (underdeveloped young develop in pouches) placentals (placenta allows long development in mother so can run when born)
primary growth: from apex and root - adds height, product of persistent embryonic region called meristem,
aerobic respiration: glucose is oxidized, O2 plays the role of the terminal electron (reduced) acceptor which creates water, NADH is oxidized to give electrons to the ETC
animal domestication: genetic change making animals more amenable to humans, should be: docile, non-territorial, dominance hierarchy, uninhibited breeding, rapid growth
endosymbiont deterioration, replacement and compensation: endosymbiont's genome is reduced, second endosymbiont can be accepted, or bits of endosymbionts DNA can be transferred to the hosts nuclear genome
hominid: upright walking primate, moved out of africa super early,
yeasts: unicellular fungi, not monophyletic, found in all fungal lineages
genome relationships: not related to replication speed, related to cell size, some relationship with extinction rate
chromosomes: prokaryotes - one circular with one origin of replication, eukaryotes - multiple linear with many origins of replication
cambrian explosion: one time event 524 million years ago in which all existing animal phyla appear in the fossil record, explained by high levels of oxygen, origin of HOX genes, many species appeared at the same time and aren't related to eachother
mycorrhizae: endophytesfungal symbiosis with roots, ecto - sheath around outside of roots, endo - hyphae penetrate root cells, increases surface area of plant cells, 90% of plants have them
secondary growth: adds girth through vascular cambrium, produces phloem on the outside, xylem on the inside
5 Steps of Adaptive Radiation: 1. species in resource rich environment 2. speciation occurs 3. Resources become scarce 4. species partition to minimize interactions 5. species adapt to new niches
charophytes: green algae ancestor of the land plants, haplontic life style - multicellular haploid organism, mitosis to make gametes, swimming sperm dispersed/fertilized to form diploid zygote, zygote first does meiosis to form haploid organism which is then built mostly from mitosis
two major innovations of seed plants: to help aid movement onto land - seeds and pollen
polyphyletic: some of the descendants of two or more ancestors (e.g. flying mammals)
transformation: incorporating DNA from a lysed cell
cis regulation: done by nearby genes, allows for tissue differentiation - possibly underlies diversity in morphological form
Ediacara: complex networks of large tubes, first macroscopic life, went extinct, not really sure what they are or what group to put them in
agriculture's impacts on biological diversity: land conversion, climate change, alteration of nutrient cycles through pollution, introduction of invasive species, biggest is allowing population growth
hydrogenosome: organelle in some amitochondriate eukaryotes that produces H2 in a fermentive reaction, suggests that eukaryotic cell formed when fermentive H2 producing bacteria got with a methanogen (uses H2 as a substrate)
closer islands: have more species than father ones of the same size
species: reproductively isolated population whose members can interbreed freely under natural conditions
features for good terminal electron acceptor: Abundant, produces non toxic product
carrying capacity: (K) maximum number of species an environment can support
density independent factors: affect birth and death rates regardless of density - like weather
bryophytes: three lineages of land plants sharing many features, models for first land plants: small, boundary layer, dissecation tolerant, thin - CO2 uptake through surfaces, limited ability to control water loss/transport water internally, water transported externally,
halobacterium: light driven proton pump, light causes confirmational change in pigment which forces a proton across the membrane
Origin of Life (time): 3.75 billion years ago
commensalism: one benefits, other unaffected - cattle egrets foraging for insects under large animals
most oxidized molecule: CO2
endophyte: fungal symbiont residing in a plant that protects the plant from herbivores and pathogens, vertically transmitted through seeds or horizontally transmitted through spores
invasion of european herbivores: europeans remove native herbivores that eat exotic plants and replace them with exotic herbivores that eat native plants, plants susceptible to herbivores they aren't selected to resist,
prokaryotes obtain materials from environment: through absorbtion across plasma membranes, no active predation, use flagella to move towards certain chemicals
causes of speciation: genetic variation, chance, natural selection (consistently greater contribution to ecological advantage to some genetic variations_
analogous: similarity in features due to convergent evolution i.e. wings in birds and bats
antheridia: sex organs where sperm are made by mitosis
intrinsic rate of increase: r (b-d) at it's highest value in optimal conditions, characteristic of species
Gaia Hypothesis: earth has co-evolved with the species inhabiting it
cellulose ethanol: made from biomass rich cell walls of plants, corn seeds are used, removes valuable nutrients from farms, it takes energy to separate lignin from cellulose in cell walls, challenge is dealing complexity of plant cell walls,
heterotrophs: other-feeders, get carbon in reduced from from biomolecues made by other organisms
domestication of plants: very few - big three = wheat, corn, rice, seed gathering efforts originally selected domesticated species,
pollen: male gametophyte develops within the wall of the haploid spore, effective way to transfer sperm in a dry wolrd
agriculture's affects on climate change: 1/3!!! 25% of CO2 emissions, 54% of methane production, 80% of nitrous oxide
lichen: symbiosis between algae and fungi
club mosses/ferns: major part of life cycle is sporophyte, spores produced by meiosis - germinate to form a bisexual gametophyte which will produce alternating generations of eggs and sperm,
selfish operon theory: operons are the outcomes of lots of HGT, maintenance of operons function promoted by selecting for clustering
farming: central biological/ecological relationship in settled society, aggresive manipulation of plants and animals, most profound way humans have changed the world,
reducing agents: coenzymes that transfer electrons and energy
athropod characteristics: jointed apendates, chitinou exoskeleton, dorsal heart, open circulatory system, ventral nerve chord
why have sex?: dilutes inheritance so must have great return, allows for random separation of chromosome pairs - TINY odds of recreating own genetic make up, lining up of chromosome allows for crossing over and more diversity
reduction: oxidation number decreased, gain electrons, energy stored
central Dogma of genetics: DNA stores info, RNA transcribes that code into a protein, cannot be reversed if mistakes are made
nitrogenase: enzyme with energy intensive redox reaction, inactivated by the presence of O2
operon: one stretch of DNA that encodes for several proteins regulated together, 50% of prok genomes are organized this way, contains protein coding genes and necessary regulatory genes
roots: specialized surfaces for the uptake of nutrients, enhanced by fungal symbionts, very old relationship,
amitochondriate eukaryotes: lack mitochondria, display simple cell structure because they rely on hosts for food and protection
evidence of direct human impact on large mammals: high percentage of extinctions where humans arrived - lower where humans evolved, strong correlation in time, mammals who most recently experience humans have highest extinction rates
Methanogens: anaerobic Archaea that oxidize hydrogen and reduce the electron acceptor CO2 to create methane, produces little ATP compared to aerobic respiration but CO2 used to be only oxidized molecule readily available
ferementation: only uses substrate level phosphorylation, does not involve transfer of electrons, gets energy from oxidation or organic compounds using an endogenous electron acceptor, no transfer of electrons or energy, organic molecule is rearranged so that there is less energy stored in the bonds of the product
domestication syndrome: increased seed size w/ thin seed coat, delay in seed opening at ripening, larger fruit, thicker rinds, loss of self-seeding ability
two themes of evolutionary history: cumulative nature of biological diversity, coevolution of earth and life
kinds of natural selection: stabilizing (higher frequency of good variant from larger spectrum), directional (shifts entire spectrum towards good end), disruptive (shifts towards two good variants promoting stable divergence)
logistic growth: S shaped curve more closely resmebles natural populations, ΔN/Δt = r[(K - N)/K]N , growth slows as it approaches K, stops when N=K
farming pre 1825: ploughing, irrigation, terracing, agricultural practices to maintain soil diversity,
oxygenic photosynthesis: oxidize water to reduce NADP and make NADPH, produces Oxygen and protons, light absorbed twice to span energy gap from H2O to NADP
simple islands (hosts): have fewer number of species
heredity: storage, transmission, implementation of information
four main biomolecules: carbohydrates, proteins, lipids, nucleic acids
founder effect: small populations colonizing an island can display biased proportions leading to changes in speciation
operational genes: code for specific metabolic functions - horizontally transferred,
evolution of complex multicellularity: 500 million years ago
Ranking of Large/small and near/far islands in terms of numbers of species: SF, LF, SN, LN
carbon fixation: creating dissolved organic molecules from gaseous carbon, improving the ability of carbon to make higher energy bonds
functional response: increased response of predators because of increased ease of encounters with prey, a fast response, increased rate of predation
prokaryotic genome: one, small, circular chromosome
order of hominid evolution: Australopithecus afarensis, habilis, egaster, meanderthalensis, erectus, sapien,
definition of life: information and metabolism
harvest index: amount harvested::amount produced
industrial nitrogen fixation: Haber-Bosch process created in 1908, 1% of total energy use, almost as much as terrestrial biological nitrogen fixation
effects on population densities: abundant resource users higher, small individuals higher, newly introduced species w/o natural enemies higher, one's with complex social organizations higher
complex vs. simple multicellularity: all have molecular adhesion, communication/transfer of resources, predator avoidance and positional benefits, only complex has inside and outside
introns/exons: introns - noncoding sequences that are spliced out, permit exon shuffling (group II remove themselves pre-translation while splicosomal ones are removed by the splicosom in euks), exons - coding regions spliced together, noncontinuous coding allows for differential splicing and therefore more diversity
why be haploid?: small, higher S::V ratio, easier to replicate, more efficiently remove deleterious mutations - haploid populations with few mutations and higher fitness
cell nucleas: distinctive feature of eukaryotes, separates DNA transcription from DNA translation allowing for RNA processing to occur
positive feedback loop in r-selected species: mice eat moth pupae, moths eat oak leaves and affect acorn populations, which affect mouse populations
two main forms of energy used by organsisms: sunlight and energy
gene duplication: can be seen as a foundation for biological diversity, only need one working copy, the other can mutate, sometimes causes retrotranscription,
multicellular sporophyte: amplifies the number of spores that can be produced, assists with dispersal, spores important because fertilization on land is a rare event and can grow into an adult without fusing with another cell
conjugation: connection formed through which chromosomes and plasmids are transferred
amensalism: one harmed, other unarmed (accidental like tree branches falling)
Seeds: spores producing female gametophytes are not dispersed, remain on sporophyte to be nourished, seed - diploid covering, haploid female gametophyte, diploid embryo,
yeasts: unicellular fungi
xylem: axial tubes for water transport through hollow cells w/o cytoplasm, water pulled through by capillary forces, travels through cells that have been programed for death
life outside the boundary layer: can compete better for sunlight, better dispersal, ability to control water loss, internalization of CO2 uptake surfaces, internal transport tissues, tissues specialized for support and stability
electron donors in photosyn: prevent cholorphyll from staying bleached
3 stages of carbon fixation: 1. fixation (carbon enters) 2. reduction (energy transferred, carbohydrates withdrawn) 3. regeneration of RuBP
explanation of metabolic diversity: operons and horizontal gene transfer
Rubisco's substrates: RuBP and CO2
major changes from apes to humans: brain increase in size, brow shrinks as forehead becomes more prominent, teeth shrink, face flat
sythesizing ATP: 1. substrate level phosphorylation (fermenters only do this) 2. Oxidative Phosphorylation
exponential growth: constant birth and death rates, j-shaped curve,(change in population)/(change in time)=(b-d)N, invasive species/pests/pathogens often experience exponential growth = r-selected species because only limited by their growth rate (r)
secondary symbionts: facultative for host, reside in many tissues, more invasive, plastic genomes - uptake/rearrangement, yougner
evolutionary rule: smaller speices show more taxon and tissue conservatism
characteristics of prokaryotes: small cell size yield high surface area::volume, small genome with small circular chromosomes, simple structure without endo-membrane system, producers of over half of earth's primary productivity
oxidative phosphorylation: sunlight pumping protons across membrane to create ATP, photon hits chl exciting a resting electron that is transfered to the ETC
chemolithotrophs: obtain energy from inorganic sources to make ATP and NADP if autotrophic
chemoorganotrophs: use organic compounds as source of energy and reduced carbon, use energy in stored bonds to create ATP
bryophytes: first lineage of embryophytes, avoid self-fertilization by gendering gametophytes, embryo is retained and becomes diploid sporophyte that produces spores by meiosis, spore germinates to produce multicellular haploid gametophyte which makes gametes my mitosis, swim together to fertilize, embryo retained and goes through mitosis to make multicellular sporphyte
two modes of using sunlight: 1. use it to make atp and obtain carbon from organic molecues heterotrophically 2. use sunlight to make ATP and NADPH (called photoautotrophy)
eukaryotic genetic features: large, linear chromosome, specialized for sex and recombination, gene regulation occurs, good at augmenting informational content of genome
problem with complex multicellularity: need solution to diffusion problems, diffustion time proportional to distance squared, vascular systems
r selected species: producing as much offspring as you can in risky environments, no influence over which offspring survive, grow exponentially, far from K, regularly decimated by harsh environment,
hyphae: long really skinny cells with high surface to volume ratio - well suited for absorptive heterotrophy, facilitates decomposition and paracitism, similar to pollen tubes/root hairs, incompletely divided cells, continuous cytoplasm with just enough space for nucleas
top down: predators/parasites regulate herbivores that influence plant competition
human phylogeny: orangutans, gorillas, chimps, humans
respiration: oxidizing organic molecules all the way to CO23 and running electrons through an electron transport chaint o terminal electron acceptor
biodeisel challenges: made from soybeans - directly competes with food production, amount limitations - if entire us corn crop used for ethanol would provide 12% of liquid fuel demand,
adaptive value of musicality: way to manipulate emotional states in harsh conditions, foster communities, could be auditory cheesecake (pinker), community cohesion is advantageous when small social groups compete for resources - keeps members in same emotional state, useful for when exploring america,
density dependent factors: b and d fluctuate in response to changes in N, diseases spread more easily in dense populations, desnse populations reduce amount of food each individual gets
effects of salinization: shown by comparison of Sumer and Egypt, agriculture salinates water and brings up water table - productivity lost, quick flowing nile doesn't bring as much dissolved material - irrigated agricultural lasted for centuries with no salinization
Origin of Eukaryotes: 2.5 billion years ago
anoxygenic photosynthesis: oxidize something other than water to reduce NADP
grasses: 1/3 of lands vegetation, would return to forest but constantly beat down, fine for them - they grow from bottoms,
k selected species: investing resources in long-term development, best for predictable environments, remain close to carrying capacity, limited resources and strong competition, survival of the fittest
Neolithic revolution: 10 centers of independent development of domestication, four explanations: 1. cultural progress 2. environmental change/instability 3. population pressure-wild resources becoming scare makes agriculture seem like a good idea 4. coeveolution
energy inputs for growing crops: sunlight, human/animal labor, fossil fuels: fertilizers, irrigation, pest control, weed control, storage, transportation, all provide greater resource availability and reduce competition,
autotrophs: self-feeders, make biomolecules from scratch, found in all branches, major work of making triple bonded N useable, chemolithotrophs and phototrophs
obligate symbionts: show co-speciation in phylogenies
mushroom life cycles: bodies made of hyphae, mycelium - simple multicellularity, mostly haplontic, haploid spores formed by meiosis, germinate into haploid mycelium, plasmogamy fuses cytoplasms to create dikaryote state (n+n) with distinct nuclei kept in order by camp connexions, karyogamy - fusion of nuclei to create diploid zygote which immediately makes spores
Biota of a place results from: historical (timing and separation of the place, origin of a group of organisms), ecological (size and distance of a place from source of colonists), evolutionary (complexity and opportunities for speciation)
C-value paradox: mismatch between complexity and genome size
herbivores: often caught in the middle, affect plants by 1. decimation, 2. shifting competition balance, 3. causing habitat specialization, herbivory is expensive for plants, sometimes promote plants, sometimes deter them
archegonia: sex organs where eggs are made by mitosis
phloem: aial tubes for carbohydrate transport, occurs in highly modified living cells, sugars pushed through by osmotic pressures
syntropy: organism relies metabolism of another organism to run its own metabolism, e.g. fermenters in plant cell walls
mutualisms: both gain
limits on feeding 10 billion: energy availability (modern agriculture has heavy dependence on fossil fuels) water (#1 issue facing future food production) competition for land (urbanization, biofuels = fossil fuels vs. food) fertilizer availability (plants also need phosphorous which is limited and has no HB process) land degradation (lose of land due to agriculture, fertile land is precious from salinization and erosion)
farming 1825-1927: significant rise of food supply mainly due to increase of arable land, beginnings of agricultural research
avoiding acoustic competition: shift (timing, frequency, loudness, geographical range)
angiosperms: best water transportation systems - biggest xylem vessels,
greenhouse gas effect: energy in from sun passes through atmosphere, warms earth, reflects of green house gasses and comes back down, transparent to short wave, absorb long wave,
Adaptive Radiation: rapid divergence of species from one single ancestor into many descendent species, each adapted to use different habitat or resource, usually in environments formerly unreachable
parasitism/predator-prey: one gains, one suffers
Hierarchical Ranks: King Phillip Came Over For Good Sex
farming 1927-1960: mechanization dictates increasing dependance on off-farm inputs, nitrogen fertilizers replacing organic manures, chemicals for weed control introduced,
Chordates: our closest relatives, notochord allows for wave like body movements, pharyngeal slits, dorsal hollow nerve chord, muscular post anal tail,
numerical response: increased total consumption because of increased survivorship, slower, increase in the number of predators
why be diploid?: sometimes useful deleterious mutations, increased adaptation speed, speedier acquisition of new functions
prokaryotes competing for resources: grow faster to create more surface area for absorbtion - requires a lot of cell division, in abundant resources growth rate limited by sped of DNA replication
oxidation: oxidation number increased, lose electrons, energy released
phylogeny as a hypothesis: best description of things that happened in the past based on all the data we have
amniotes: completely left the water, internal fertilization allows for development of semipermiable egg shells, can get away from the water, larger body size
difference between ATP and NADP: NADP is a reducing enzyme that transfers electrons and energy, to reduce a compound, ATP transfers high energy phosphates, cannot be used to reduce another molecule
mutations: change in the DNA sequences of genes, often deleterious when it does happen, chance proposes, selection disposes
direct development: in tetrapods larval fish like stage develops in the embryo and adult stage emerges, allows for mating out of the water
homologous: similarity in features due to common ancestry i.e. bone structure in bats and birds
Hox Genes (homeotic genes): control main body axis of animals, defines a position or region on the embryo, transcription factors regulate expressions of genes and therefore size/types of structure
self fertilization in seed plants: not a problem - spores produced by meiosis - 2^n possibilities
adaptations to control water loss: stomata, cuticle
Bilaterial animals: protostome (mouth forms first in embryo) and deuterstomes (anus forms first in embryo)
C4 photosynthesis: two types of cells work together to overcome low concentration of CO2, concentrates CO2 at rubisco, costly - only plants in high light concentrations can afford, allows plants to be more efficient in terms of water - can keep stomata closed because CO2 concentrations don't matter, large portion of food we eat is made in this way
woronin bodies: sealing mechanisms that plug up hyphae holes to prevent damage
paraphyletic group: contains some but no all of the descendants of a single ancestor (e.g. fish in the taxonomy of vertebrates)
trans-regulation: done at a distance and less well understood,
competition: both sides are harmed
Second Law of Thermodynamics: most energy consumed is lost to respiration - only 10% becomes available for the next trophic level
determinants of species ranges: historical processes, dispersal ability, interactions with other species, limits to adability to abiotic conditions
protozoa: unicellular eukaryotes that lack a cell wall, allows for option of predation
problems for plants on land: low CO2 - much more dissolved in the oceans - every photosynthetic cell must be in contact with the environment, need support structures
oxygen levels reach 1%: 2.4 billion years ago
malthus vs. boserup: food controls population limits vs. populations control food amounts, issue is complicated by science/technology/human intervention

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