entire bio 108 units

USE THIS TO STUDY FOR FINAL - still need to add unit 1 I think?

define amniotes

group of tetrapods whose extant members are reptiles and mammals (birds included). Key unifying adaptation is the amniotic egg.

amniote shared derived trait

amniotic egg. enables reproduction on land by providing: Gas exchange, and preventing water loss (02, CO2), nutrient supply - provided by the yolk sac and albumen. waste removal - managed by the allantois.

Protection: from desiccation: achieved by the amniotic membrane, chorion, and external shell. From mechanical shock: cushioned by the amniotic fluid

laying amniotic eggs

the amniotic egg is an adaption for laying ends on land. sexual reproduction is independent of water, the fluid filled cavity replaces the aquatic environment. Laying eggs on land (often buried) or retain fertilized eggs internally.

Internal fertilization - shared derived characteristic amniote

internal fertilization via specialized intermittent organs. Intermittent organ is an external genitalic organ of males that is specialized for sperm delivery during copulation.

direct development - shared derived characteristic of amniotes

amniotes develop directly into terrestrial forms without aquatic larval stages or metamorphosis (ex turtles)

amniote adaption for terrestrial life

water retention - thick layers and impermeable skin, reduces water loss while preventing dehydration

efficient lung ventilation - axial skeletal muscles associated with the rib cage power lung ventilation contrasting with the inefficient buccal pump mechanism used by amphibians

classification of amniotes

we can look at cranial opening near the eye sockets.

Anapsid: lacks temporal fenestrate (turtles)

diapsid: two pairs of temporal fenestra behind the eye sockets (reptiles)

synapsid: one pair of temporal fenestra (mammals)

characteristics of non-avian reptiles

skin protection and shedding: thick dry keratinous scaled, composed of beta keratin, which is waterproof and resistant to abrasion.

reproduction adaptions: reptiles typically lay eggs encased in leathery shells, burying them. Crocs care for babies

circulatory system and thermoregulation in non-avian reptiles

three chambered hearts, similar to amphibians. as exothermic animals, they rely on external heat to regulate body temperature. lower metabolic rates and reduced food intake due to getting energy from sun

permian diversification

the collapse of carboniferous rainforest created a cooler dryer climate in the permian driving reptiles to adapt to new terrestrial habitats. The end permian extinction eliminated dominant synapsids. Opened ecological niches allowing reptiles to evolve and dominate terrestrial ecosystems during Mesozoic era

two primary lineages of diapsids

lepidosaures: lizards snakes. Archosaur: crocodilians and dinosaurs

turtles and tortoises

herbivory and carnivore, anapsid skull (no large opening behind eyes). bony cartilaginous shell, fused to vertebrae clavicle and ribs. teeth lost - replaced with toothless beaks. Males have single internalized penis

lepidosaurs

teeth fused to their jaw, bodies covered in scales. Males have hemipenis (two).

tuataras: ancient lineage of lepidosuars, highly endangered. lack intermittent organ (no penis)

squamates: dominant extant lineage of lepidosaurs (lizards and snakes), loose jointed jaw and skull, hemipenis, periodic moulting (lose skin)

lizards

external ears, well developed limbs (legless lizards are real developed independantly), feeding behaviour, swelling chunks whole due to lack of teeth.

snakes:

ancient group of squamates, monophyletic group of legless lepidosaues that evolved from burrowing lizards. no external limbs, capture and consume prey with loose haw and skull bones (kinetic skull) and elastic skin. venom, squeeze or swallow alive.

snakes vs legless lizards

monophyletic group, and adaption of legless lizards which developed independently

oder crocodilia - Archosaurs

reptiles characterized by socketed teeth which are not fused to the jaw. the two extant lineages are crocs and birds which share a common ancestor! crocodilians also swallow prey whole, birds and crocs developed independently, allowing a four chambered heart (unique feature), single intromittenet organ, maternal care behaviours as well.

extinct reptiles

Ichthyosaurs ("fish-lizard") were dolphin-like marine reptiles that reached up to 15 m in length. Plesiosaurs ("near-lizards") were flippered marine reptiles with small heads, long necks, and slender tails, ranging from 2 to 14 m in length. Pterosaurs with membranous wings are one of the three independent origins of true (flapping) flight among vertebrates. Non-avian dinosaurs were a diverse group, including some of the largest terrestrial animals to have ever existed

Ichthyostega

one of the first amphibians. semi terrestrial tetrapod with an amphibian like body plan

extant amphibians

form a monophyletic group of terrestrial or freshwater tetrapods

describe the characteristics of extant amphibians

thin mois skin, permeable to water and gases. no scales ("naked"), little keratin, absorb and lose water through skin, susceptible to desiccation (therefore typically in moist habitats), sensitive to salt, contain mucous glands (produce secretions other than maintain moisture), cutaneous respiration. Ectothermic (rely on heat), low metabolic rate, behavioural thermoregulation, buccal pump. gills in aquatic stages, three chambered heart, external eardrums

where do amphibians reproduce

water or moist habitats. spawn in water (oviparous), males and females pair but fertilization is external. Eggs lack protective shells and extra embryonic membranes. Eggs are surrounded by a desiccation sensitive gelatinous coating

amphibian

"both ways of life" Refers to the metamorphosis of aquatic larvae into terrestrial adults. Most amphibians fertilize eggs in water that develop into herbivorous aquatic larvae (tadpoles) with gills and no limbs.

salamanders order urodela

amphibians with tails in the adult stage. Superficially lizard-like appearance: slender bodies, blunt snouts, and short laterally extended legs. Salamanders typically lay eggs in water and have aquatic larvae, but there's considerable variation in their life cycles. Larvae have external gills; otherwise, they resemble adults with the presence of legs

frogs order Anura

− Transform from larval tadpoles with tails to adults without tails. Frogs are characterized by their long, powerful hind legs, which are modified for jumping, although they lack legs in early larval

development stages. Frogs have well-developed ears. leathery skin = toad. feed on algae as larvae, transition to consumer invertebrates as adults

caecilians order apoda

are legless amphibians (~170 species) that superficially resemble earthworms or snakes. Most caecilians are burrowers, living in extensive networks of underground tunnels. use internal fertilization

three clades of amphibians

salamanders frogs caecilians

ectothermic

A physiological state where an animal's body temperature is primarily determined by the temperature of its surrounding environment. Most amphibians and non-avian reptiles are ectotherms.

global amphibian decline

habitat destruction, climate change, invasive species, UV radiation, pesticides, chytrid fungus (parisitic infection)

endothermic

A physiological state where an animal generates internal metabolic heat to maintain a relatively constant body temperature independently of the environment. This is a shared derived trait of birds and mammals.

bevavioural thermoregulation

The use of specific behaviours to regulate body temperature. For amphibians, this often involves moving between sun and shade or into water to prevent overheating or desiccation.

permeable skin

Thin, "naked" skin (lacking scales) that is highly permeable to water and gases. It allows for cutaneous respiration but makes amphibians highly susceptible to desiccation.

cutaneous respiration

the process of exchanging oxygen and carbon dioxide across the moist, vascularized skin. In many amphibians, this complements or replaces gas exchange via lungs.

mucous glands

Specialized glands in the skin that secrete mucus to maintain moisture, which is essential for both protection and cutaneous respiration.

three chambered heart

A heart consisting of two atria and one ventricle. While it allows for double circulation, some mixing of oxygenated and deoxygenated blood occurs in the single ventricle.

metamorphis

A distinct post-embryonic developmental stage where a larval form (e.g. a tadpole) undergoes significant morphological and physiological changes to become an adult.

external fertilization

A reproductive strategy where eggs are fertilized by sperm outside the female's body, typically in a moist or aquatic environment to prevent the gametes from drying out.

oviparous

A mode of reproduction in which the animal lays eggs that develop and hatch outside the mother's body.

dual life cycle

Refers to the "double life" of many amphibians, beginning as an aquatic larva with gills and transitioning to a terrestrial or semi-terrestrial adult with lungs.

are viruses alive?

depends. they cannot reproduce by themselves due to needing a host cell. we cannot trace the lineage due to not forming fossils

eukaryotic cells differ from prokaryotic cells:

1. DNA in linear chromosomes in contained membrane bound nucleus

2. membrane bound organelles

3. eukaryotic are usually larger

4. cytoskeleton and dynamic membrane that facilitates movement and feeding (phagocytosis)

5. eukaryotes undergo meiosis and fertilization, promoting genetic diversity

define endosymbiosis

symbiosis between two species in which one organism lives inside another organisms cell or tissues

serial endosymbiotic theory

1. ancestral porlaryotic cells gradually developed end-membrane system,s through infolding of her plasma membrane giving rise to endoplasmic reticulum and nuclear envelope

2. Ancestral prokaryotic cells formed an endosymbiotic relationship with an aerobic (oxygen-utilizing), heterotrophic prokaryote, likely an

α-proteobacterium

3. A lineage of ancestral heterotrophic eukaryotes acquired an additional endosymbiont, a photosynthetic prokaryote (photoautotroph), a cyanobacterium.

advantages of multicellularity:

• each cell can take unique functions. ( specialization)

• increased size and complexity

• extended lifespan - larger organisms often live longer

• predation avoidance - structural complexity helps larger organisms evade predators

evidence of the endosymbiotic theory

1. 1. mitochondria and chloroplast share structural similarities with bacteria

   2. mitochondrial genomes are most similar to alpha- proteobacteria and chloroplast genomes to cyanobacteria

   3. mitochondria and chloroplasts replicate independlty in eularyotics

   4. mitochondria and chloroplasts have separate protein synthesis machinery (ribosomes)

three domains of life

Bacteria, Archaea, and Eukarya

• there is evidence of significant genitive exchange between the domains

organ of multicellularity

evolved independently in multiple lineages, giving rise to algae plants fungi and animals

horizontal gene trasnfer

• origin of eukaryotes

• - photosynthetic processes

  • the non-reproductive movement of genetic material between organisms, allowing rapid acquisition of new traits like antibiotic resistance

protists

informal term for a diverse group of mostly unicellular eukaryotes

• not a monophyletic group

• "junk drawer of eukaryote"

• definition by exclusion: not animals, not plants, not fungi

• structural diversity nutritional diversity

protist diversity

photoautotrophs- use chloroplast to fix inorganic carbon using light energy

chemoheterotrophs - absorbs organic molecules or ingest larger food particles

mixotrophs - can switch between the two above

Excavata

group of unicellular protist characterized by modified mitochondria and unique flagella

SAR

protists are classified based on DNA similarities and likely evolved through 2 endosymbiosis. SAR includes both uni and multi cellular protests, particularly abundant in the ocean ecosystem

Archaeplastida

uni and multicellular photoautotrophs, including red and green algae and plants

Unikonta

chemoheterotrophic protists which include multicellular fungi and animals as their descendants

clade excavata

• modified mitochondria or dinsiticive flagella

• unicellular

• diplomanads, parabasalids - (uni) , euglenozoans

• lack a unifying set of cytoskeleton structures

• para commonly found in anaerobic environments

• eug presence of spiral or rod which is unknown function inside their flagella

• subgroups: Kinetoplastids, and Euglenids

SAR clade

Stramenopiles, Alveolates, and Rhisarians

• unified through DNA similarities

• secondary endosymbiosis origination

age of fossils

sedimentary strata reveals relative age ( due to layers)

radioactive decay of isotopes: carbon dating (half lives)

important events in history of life

4.6 bil: formation of earth (Hadean Eon)

3.9 bil: 1st life replicating molecule

3.5: first prokaryotic single celled

2.7: 02 in atmosphere from photosynthesis

1.8: first eukaryotic single celled

1.3: first multicellular eukaryotic cell

535 million: Cambrian explosion

500 mil: colonization of land by fungi plants and animals

life:

organized, metabolism, response to stimuli, homeostasis, adaption, reproduction

geological records:

divided into Archaean, Proterozoic, and Phanerozoic

Precambrian = Archaean + Proterozoic

Describe the uses and limitations of the fossil record.

• provide direct evidence of evolutionary history. Fossils are preserved remains or organisms. Fossils are used to calibrate phylogenies

• fossil record is biased and incomplete. fossils only preserve the hard part of the organisms

• associated with sedimentary rocks ( distinct layers of rocks are called strata)

type of fossils

mold fossils: hollow space remains after the organism decays

casat fossil: forms when minerals fill the hollow space

preserved fossils: retain much of the original organic material of the organism ( carbon films)
trace fossils: provides evidence of an organism behaviour such as tracks, faces, or burrows

Phanerozoic period

last half billion years

• multicellular and eukaryotic cell life

• divided into: Palaeozoic, Mesozoic, and Cenozoic

Explain the causes and impact of Permian extinctions.

• defines the boundary between Paleozoic and Mesozoic era (252 mya)

• rapid most severe event

• cause is unknown but best supported hypothesis is due to catastrophic environmental change caused by volcanic activity

Explain the causes and impact of Cretaceous extinctions.

• 66 mya separates the Mesozoic era from the Cenozoic

• 50% of marine species went extinct

• coincides with meteorite impact in Mexico

Describe events leading to adaptive radiation.

1. mass extinction can lead to adaptive radiation- by eliminating species mass extinctions can prepare for adaptive rad

   - ex: adaptive radiation of mammals following extinction of dinosaurs

   2. evolution of novel characteristics:

   - when organisms colonize new environments that have little competition

   - ex: Hawaiian plants

Outline the hypothesized sequence of events leading to life.

1. abiotic synthesis of small organic molecules

2. 2. polymerization o small organic molecules into organic polymers

   3. formation of protocells

   4. emergence of self replicating molecules

Holocene extinction

• human causes 6th mass extinction

• driven by population growth and overconsumption of earths resources

• biodiversity is declining faster now than ever before

abiotic synthesis of small organic molecules

primitive atmosphere was weakling reducing or neutral. instead of frying into the atmosphere abbot synthesis may have occurred near volcanoes or deep sea hydrothermal vents where strongly reducing conditions are found’

Miller - Urey demonstrated that organic molecules can be produced spontaneously from simple molecules in various 02- free environments

polymerization of small organic molecules

small organic molecules can undergo polymerization reactions when they join together to form larger organic molecules or polymers

ex: amino acids form peptide bonds through condensation reactions creating polypeptide chains

• this process likely occurred on hot surfaces (clay, rock or sand)

protocells

free floating amino acids, would not have been able to behave life cells. In water lipids and other organic molecules can form hollow vesicles with lipid bilayer

• protocells are simple cell like structures that form when organic molecules become enclosed within membrane vesicles

emergence of self replicating molecules

• which could store and transmit information much life mode DNA or RNA is a defining feature of life

• natural selection led to the emergence of self replicating RNA molecules. ribomses are the RNA molecules catalyst

oldest known fossil

stromatolites

oxygen revolution

when oxygen became accumulating in atmosphere and oceans. Cyanobacteria evolved to use the suns energy … photosynthesis

• initially 02 produced cyanobacteria reacted with iron dissolved in oceans

• early prok evolved in oceans with no oxygen and relied on anaerobic metabolism to obtain energy without oxygen

• 2.7 to 2.3 bya causing extinction of many prokaryotic groups

structural and functional adaptions that contributes to prokaryotic success

1. cell surface structures:

2. metabolically inactive endospores

   3. motility (flagella and taxis)

   4. simple internal organization and DNA

   - prokaryotic cells lack cellular compartmentalization

   - single circular chromosome not bound by a nuclear membrane

structural and functional adaptions prokaryotic (cell surface)

cell wall: peptidoglycan is present in the cell walls of bacteria but absent from cell walls of archaea

- gram staining: Gram-positive bacteria with thick peptidoglycan layers, Gram-negative bacteria with thinner peptidoglycan and an outer lipopolysaccharide membrane.

- capsule: a sticky outer layer polysaccharides or proteins corroding cell wall, capsule helps protect against desiccation and help some pathogenic bacteria evade the immune system

-pili are longer and allow exchange of DNA between cells

structural and functional adaptions prokaryotic (endospores)

− Many prokaryotes form metabolically inactive endospores

that can survive extreme conditions for long periods (up to centuries).

• Endospores form when environmental conditions become unfavourable, such as during extreme temperatures or a lack of nutrients

• Endospores have tough, protective coatings that protect cells from extreme heat, desiccation, and chemical stress, allowing prokaryotes to remain in a dormant state until conditions improve.

structural and functional adaptions prokaryotic (motility)

− About half of all prokaryotes are motile (the ability to move actively), often using flagella for locomotion.

Flagella are long, whip-like appendages that are distributed across the cell surface or are concentrated at one or both ends of the cell.

− Prokaryotes can move in response to environmental stimuli, a behaviour known as taxis, moving towards or away from a stimulus

structural and functional adaptions prokaryotic (simple internal)

Prokaryotes have simple internal structures without complex compartmentalization.

− Prokaryotes lack membrane-enclosed organelles, which means they do not have distinct nuclei, mitochondria, or chloroplasts.

− Some prokaryotes do have specialized membranes that serve specific metabolic functions.

- These specialized membranes are typically infoldings of the plasma membrane.

prokaryotic reproduction and genetic diversity

• reproduce rapidly by binary fission, which is a form os asexial reproduction where a single prokaryotic cell fives into two identical cells

how do prokaryotic exhibit genetic diversity

1. Rapid reproduction (short generation times).

2. Mutations: mutation rates during binary fission are low, but the high reproduction rate means mutations accumulate quickly in prokaryotic populations.

   3. Genetic recombination by horizontal gene transfer: transformation, transduction, and conjugation.

genetic recombination

Prokaryotes can undergo genetic recombination, where genetic material from one cell is incorporated into another cell.

- Genetic recombination contributes to the genetic diversity of prokaryotes.

- Unlike eukaryotes, prokaryotic genetic recombination is not tied to meiosis.

- In prokaryotes, genetic recombination between individuals requires horizontal gene transfer(HGT); binary fission involves only vertical inheritance and no recombination.

− Horizontal gene transfer(HGT) is the movement of genetic material between cells by mechanisms other than parent-to-offspring inheritance (e.g. transformation, transduction, and conjugation).

mutations

Mutations accumulate quickly in prokaryotic populations.

• Although the per-cell-division mutation rates in prokaryotes are similar to or lower than those of multicellular eukaryotes, bacteria have very short generation times (rapid reproduction) and enormous population sizes; they generate far more mutations per unit time.

• The combined effect of mutations and rapid reproduction contributes to substantial genetic diversity within prokaryotic populations, enabling rapid evolution

prokaryotes

microscopic organisms, contribute to around 14% global biomass

highly adaptable thrive in diverse environments

- earths earliest life form evolved from Archaea and bacteria

- lack nucleus

prokaryotic genetic diversity

1. rapid reproduction (binary fission)

2. 2.mutations - accumulate quickly

   3. genetic recombination in prokaryotes - genetic material from one cell is incorporated into another cell

horizontal gene transfers

movement of genetic material between cells by mechanisms other than parent to offspring inheritance

ex: transformation, transduction, and conjugation

binary fission

A form of asexual reproduction where a single prokaryotic cell divides into two identical cells. This process allows for rapid population growth in favourable environments.

peptidoglycan

A structural polymer consisting of modified sugars cross-linked by short polypeptides; a unique component of bacterial cell walls.

fimbriae

Short, hair-like protein appendages that allow prokaryotes to attach to surfaces or to one another (e.g. for colony formation).

specialized prokaryotic groups

Methanogens: A group of archaea named for their unique metabolism, in which they use CO2 to oxidize H2, releasing methane (CH4) as a waste product. They are strict anaerobes (poisoned by oxygen) and are commonly found in anaerobic environments such as swamps, marshes, and the digestive tracts of herbivores (e.g. cattle).

Extremophiles: Organisms, predominantly within the Domain Archaea, that thrive in conditions that would be lethal to most other life forms.

Halophiles: Organisms that live in highly saline environments (e.g. the Dead Sea).

Thermophiles: Organisms that thrive in very hot environments (e.g. volcanic springs).

define ecological interactions involving prokaryotes

energy source light = phototrophs

energy source chemical = chemotrophs

heterotrophs = obtain carbon by consumer organic matter

autotrophs= inorganic matter

transformation:

where prokaryotic cells takes up and intergrades foreign DNA from its external environment

transduction

the transfer of DNA via bacteriophages (viruses that infect prokaryotes)

conjugation:

direct transfer of DNA usually plasmid, between cells via a plus

• a donor cell transfer DNSA to recipient cell

• transfer of genetic material during conjugation is unidirectional occurring exclusively from the plus producing donor cell to the recipient cell

• plasmas are usually transferred during conjugation

prokaryotes metabolic diversity

obligate aerobes: rely on 02

obligate anaerobes: use fermentation

facultative anaerobes: can switch

some prokaryotes including bacteria can convert atmospheric nitrogen into ammonia through biological nitrogen fixation

prokaryote research and tech

food production, decomposing prokaryotes ( bioremediation- remove pollutants, and sewage treatment- break down organic matter in wastewater), genetic engineering

bacteria :

proteobacteria: large and group of gram negative bacteria

chlamydias: obligated and intracellular parasites that only live within animal cells

spirochetes - helical heterotrophs spiral and corkscrew like movements. free living and parasite bacteria

cyanobacteria: photosynthesis

gram positive: decomposers found in soul, pathogenic

chlamydias

• intracellular parasites that live only within animal cells.

• − Chlamydias are dependent on a host for survival and reproduction.

  − Chlamydia cell walls lack peptidoglycan (stain gram-negative).

  − Chlamydia trachomatis causes a common (STI) and contagious eye infections that can lead to blindness in both humans and animals.

spirochetes

spiral-shaped bacteria that have flexible walls and are capable of movement. are helical heterotrophs known for their spiral shape and corkscrew-like movement. Many live as free-living bacteria, but some are parasites.

symbiosis

is a close, long-term ecological relationship between two species, where at least one species benefits.

• Symbiosis typically involves a larger host and a smaller symbiont