Bio 102 final

how was early earth different from today?

it was hot, no oxygen, atmosphere was rich with byproducts from volcanic eruptions (nitrogen, methane, ammonia)

four steps to generate de novo life on earth

1. abiotic synthesis of small organic molecules
2. synthesis of macromolecule
3. generation of protocells (macromolecules packaged inside lipid vesicles)
4. origin of self-replicating, heritable macromolecules within cells to serve as the instructions for life

four eons of earth

hadean, archaean, proterozoic, phanerozoic

six major milestones of life

1. first single-celled organisms appear
2. photosynthesis and the oxygen revolution
3. first eukaryotic cells appear
4. multicellular organisms appear
5. cambrian explosion
6. colonization of land

endosymbiont theory

large prokaryote engulfs small aerobic prokaryote, all eukaryotes are descendants of that large prokaryote and maintain the smaller prokaryote as mitochondria, a eukaryotic cell engulfed a photosynthetic prokaryote which became a chloroplast

adaptive radiation

rapid evolution of diverse, novel species from a common ancestor, typically occurs following mass extinctions, evolution of advantageous traits, colonization of new habitats

homologous structures

body parts in different organisms that have a similar structure but have different functions. These structures suggest that the organisms evolved from a common ancestor.

analogous structures

structures that have similar functions in different organisms but have different evolutionary origins and structures. they evolved independently and have different bone structures.

ancestral traits

arose in an ancestor and therefore are shared with taxa outside the current clade being considered

derived traits

traits that are unique to a specific clade and not shared with ancestors outside that clade

prokaryotic cells

unicellular organisms that lack a nucleus and other membrane-bound organelles. They are typically smaller and simpler in structure than eukaryotic cells and are found in bacteria and archaea.

eukaryotic cells

cells that have a true nucleus and membrane-bound organelles. They are found in organisms such as animals, plants, fungi, and protists. Eukaryotic cells are typically larger and more complex than prokaryotic cells

why do antibiotics affect prokaryotic cells and not eukaryotic cells?

Antibiotics target prokaryotic cells by disrupting their cell wall (made of peptidoglycan) and metabolic processes, which are absent in eukaryotic cells. Eukaryotic cells have a different structure and function, making them resistant to the effects of antibiotics.

peptidoglycan

a polymer that makes up the cell wall of most bacteria. It is composed of sugars and amino acids, and provides structural support and protection to the bacterial cell.

genetic recombination: transformation

many bacterial cells can absorb free dna from their surroundings, can result in new traits

genetic recombination: transduction

viruses that infect bacteria can accidentally transfer dna from one host cell to another

genetic recombination: conjugation

direct exchange of dna between bacterial cells

archaea: extremophiles

species that can tolerate extreme conditions

\-extreme halophiles: environment with high salt concentrations

\-extreme thermophiles: environment with extremely high or low temperatures

archaea: methanogens

produce methane as a metabolic byproduct, reside in the guts of ruminants like cows to help digest cellulose, reside in the human gut to break down food, used for sewage treatment

importance of archaea

produce heat-tolerant enzymes that are useful in biomedical research, digesting compounds that no other organisms can such as toxins and heavy metal compounds, helping us understand the origins of eukaryotic cells

proteobacteria

metabolically very diverse, includes E.coli, the bacteria most closely related to those that might have given rise to the mitochondria, bacteria that fix atmospheric nitrogen

cyanobacteria

plant-like photosynthesis, hugely important ecological role in producing oxygen and acting as producers in food chains

how are prokaryotes harmful to humans?

many are pathogenic (lyme disease, tb, syphilis),

how are prokaryotes helpful to humans?

They produce atmospheric oxygen, act as producers in food chains, are critical for agriculture, antibiotic production, production of foods like yogurt and cheese, and bioremediation

how can protists be distinguished from other forms of life?

They are eukaryotic organisms that are not plants, animals, or fungi. They are unicellular or multicellular and can be heterotrophic or autotrophic. They also have a wide range of shapes, sizes, and structures.

excavata

protists: have an excavated feedin groove, have modified mitochondria, one or more flagella, genetically similar

excvata: diplomonads and parabasalids

protists: modified reduced mitochondria, many have flagella, many are parasitic

excavata: euglenozoans: kinetoplastids

have a single large mitochondrion (kinetoplast), includes aquatic species that hunt prokaryotes, includes parasites, examples of human diseases caused by these: african sleeping sickness

african sleeping sickness

caused by kinetoplastid protists called trypanosomes spread by bites from the tsetse fly. the parasite crosses the blood-brain barrier causing neurological symptoms

SAR clade

a major group of eukaryotes that includes Stramenopiles, Alveolates, and Rhizarians.

__**S**__AR: stremophiles: diatoms

abundant photosynthetic organisms that comprise a significant component of phytoplankton, characterized by tough silicon-based walls, undergo blooms following massive die offs, dead ones settle on the ocean floor creating a silica-rich layer which removes a lot of carbon dioxide from the air and goes to the ocean floor

phytoplankton

primary producers in aquatic ecosystems and produce much of earths oxygen, undergo massive population expansions called blooms

what are diatoms good for?

insecticides, toothpaste, toxic spill cleanup, filtration: water, beer, honey

S__**A**__R clade: alveolates: dinoflagellates

aqueous species, photosynthetic mixotrophs and part of plankton, responsible for the red tide

what is the red tide

caused by dinoflagellates, depletion of oxygen can suffocate other aquatic life, produce toxins, exacerbated by fertilizer runoff and increasing ocean temperatures

S__**A**__R: alveolates: apicomplexans

parasites of animals, causes malaria

S__**A**__R: alveolates: ciliates

use cilia to move and feed in aquatic environments, most are predators, include paramecium, have more than one nucleus, micronuclei are exchanged through conjugation

archaeplastida: red algae

range in color from greenish-red to bright red to nearlt black, live in warm tropical oceans at great depths, most are multicellular and reproduce sexually. EX: sushi

archaeplastida: green algae

includes unicellular, colonial, and multicellular species, found in marine, freshwater, and damp environments, reproduce both sexually and asexually. EX:single celled chlamydomonas are a popular research model to study photosynthesis, flagella structure and function, and the cell structure

fungal structure

comprised of eukaryotic cells with chitin-based cell walls, some are unicellular but most are multicellular

fungal mode of nutrition

all are heterotrophs as decomposers, mutualists, and parasites, they feed via absorption of nutrients from their environments--cells secrete enzymes into surrounding environments, enzymes break down nearby organic material into smaller molecules, smaller molecules can be absorbed across fungal cell wall

fungal body structure

most body is made of narrow threads called hyphae, most hyphae penetrate through food sources, multiple hyphae extend outward to form a mass called a mycelium, the parts that are visible are often temporary reproductive structures

fungi: zygomycetes

\-includes decomposers like mold, as well as parasites and commensal symbionts

\-can opt for either asexual or sexual reproduction but prefer asexual when conditions are favorable and when they’re not favorable they opt for sexual and produce protective reproductive structures

\-diploid zygosporangium

fungi: ascomycetes

\-decomposers, mutualists, and parasites

\-can switch between sexual or asexual reproduction, during sexual reproduction most produce sacs called asci for spore dispersal

\-includes penicillium, truffles, unicellular yeast

fungi: basidiomycetes

\-decomposers, mutualists, and parasites

\-reproduce only through sexual reproduction, the reproductive structure are what we call mushrooms

\-some form mycorrhizae where body includes specialized hyphae called haustoria that invade cells in plant roots, all vascular plants have mycorrhizae

fungi mutualistic relationship with mycorrhizae

fungi efficiently break down phosphates and minerals in soil for plants, the plants then deliver organic nutrients like sugars to the fungi

fungi mutualistic relationship with endophytes

\-all plants have endophytes within their leaves

\-produce pest deterrents and increase host plant tolerance for adverse conditions

derived traits distinguishing land plants from green algae

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bryophytes

\-basal plants

\-includes mosses, hornworts, liverworts

\-haploid gametophyte is dominant

\-sperm are flagellated therefore requires water for reproduction

\-no true organs or vasculature

seedless vascular plants

\-includes ferns

\-possess flagellated sperm therefore requires water for fertilization

\-possess vasculature (xylem and phloem) and true organs (roots and leaves)

\-dominant sporophyte (haploid gametophyte is reduced and independent of sporophyte)

seeded vascular plants

\-include gymnosperms (conifers) and angiosperms (flowering plants)

\-all produce pollen (contains haploid male reproductive structures) ovules (contains haploid female reproductive structures) and seed (contains the embryo)

\-sperm not flagellated

functions of flowers and fruit on angiosperms, how are they advantageous

flowers-include male and female reproductive structures and mediate both distribution and reception of sperm

fruit-following fertilization the ovary tissue surrounding the ovules/seeds develops into a fruit that can distribute seeds via multiple mechanisms

role of transpiration in regulating distribution of water in plants

almost all water is absorbed through the roots, xylem transports water from the roots up to above-ground tissues of the plant, the water is then pulled up through the plant, water is lost by transpiration through stomata in leaves.

how stomata affect transpiration rates

because leaves are covered in a waxy hydrophobic cuticle, nearly all water lost during transpiration exits via stomata, when they are open water can exit and carbon dioxide can enter for photosynthesis

traits shared by all animals

\-all are multicellular

\-multicellular body contains different cell types specialized for distinct functions

\-cells of the multicellular body are held tightly together

\-multicellular body must form via process of embryonic development which is controlled by genes

invertebrate animal progression of complexity

porifera, cnidaria, lophotrochozoa, ecdysozoa

porifera

\-lack true tissues

\-radial symmetry

\-bottom dwelling aquatic species

\-filter feeders: removes food from water as it passes through their body

\-sea sponges

choanocytes

\-specialized cell type in sea sponges

\-are flagellated

\-engulf food particles such as bacteria

amoebocytes

\-specialized cell type in sea sponges

\-mobile

\-can take up food and help deliver nutrients to other cell types

\-some produce tough skeletal fibers of calcium carbonate

\-stem cells

cnidaria

\-are diploblasts

\-includes jellyfish, sea anemones, and corals

\-radial symmetry

\-carnivorous predators

lophotrochozoa

\-all members are diploblasts with bilateral symmetry

\-platyhelminthes: simple flatworms, acoelomates, no true circulatory system (trematodes, tapeworms)

\-mulluscs: coelomates with multiple organ systems, includes gastropoda(snails/slugs), bivalvia (clams/oysters), cephalopods (squids/octopi)

ecdysozoa

\-triploblasts with bilateral symmetry and coeloms

\-complex internal organ systems

\-all have a cuticle and a tough external layer made of chitin protecting them from dehydration and provides structure

\-nematodes

\-arthropods: insects(bees/ants), chelicerates (spiders/scorpions), crustaceans(lobsters/shrimp), myriapods(centipedes/milipedes)

four traits shared by all chordates

\-have a notochord

\-have a dorsal, hollow nerve cord

\-have pharyngeal slits/clefts

\-have muscular, post-anal tail

notocord

\-flexible rod of mesodermal tissue that runs beneath the nerve cord and above the digestive tract

\-provides structure for chordates that lack a backbone

\-in chordates with a backbone it exists in embryos but regresses before adulthood

dorsal nerve cord

\-ectodermally-derived tube that forms along dorsal midline

\-developmental starting point of our central nervous system (brains and spinal cords)

pharyngeal slits/clefts

\-grooves in the pharynx

\-in aquatic and marine chordates they can be used for filter feeding or as gills for gas exchange

\-in chordates that evolved on land they took over new functions

muscular post-anal tail

\-important for balance and movement

\-in few species it regresses during embryonic development

why are cephalochordates chordates but not vertebrates

\-their notochord persists into adulthood and provides body structure (lancelets)

how were traits acquired through vertebrate evolution

vertebrae, jaws/mineralized skeleton, lobed fins, limb with digits, amniotic egg

how do hagfish and lampreys differ from other vertebrates

they possess cartilage-based vertebrae that grow from their notochord which they retain for support throughout their entire life.

significance of lobe-finned fishes in the evolution of tetrapods

they possess modified swim bladders that can function as primitive lungs and have lobed fins--these two traits help us understand how tetrapods evolved

derived traits of tetrapods that were advantageous to life on land

\-four limbs with digits

\-highly efficient lungs

\-neck

derived traits of amniotes that were advantageous for life on land

derived traits that distinguish humans from primates and the order in which they were acquired

\-bipedalism

\-tool use

\-reduced jaw bone

\-larger brain size

epithelial tissue

\-lines body surfaces, internal and external

\-cells are closely connected into sheets

\-cells are polarized

\-simple, stratified, pseudostratified

\-functions: protection, absorption, secretion, sensory

simple epithelia

\-only one cell layer thick

\-cuboidal epithelium: good for absorption/secretion (kidney tubules)

\-simple columnar epithelium: good for absorption/secretion (intestinal lining)

\-simple squamous epithelium: good for gas exchange (blood vessels)

stratified/pseudostratified epithelium

\-stratified squamous epithelium: layered, very protective, not good for absorption or secretion

\-pseudostratified columnar epithelium: looks layered but isn’t, good for both protection and secretion but not absorption

traditional connective tissues

\-CT proper, loose (underneath skin), and fibrous (tendons/ligaments)

\-consists of sparse cells separated by an ECM

\-for support and protection

\-often found underlying epithelia or filling space inside organs

specialized connective tissues

\-bone: support, protection, movement

\-adipose tissue (fat): protection, insulation, energy storage

\-blood: gas exchange (red blood cells), clotting (platelets), protection (immune system--white blood cells)

\-cartilage: flexible support, protection

muscle tissues

\-skeletal muscle: voluntary movement in coordination with skeleton

\-smooth muscle: digestion and circulation

\-cardiac muscle: heartbeat (circulation)

nervous tissue

\-transmission of information and instruction

\-found throughout central nervous system (brain/spinal cord) and peripheral nervous system (nerves extending to/from muscles and organs)

\-neurons: transmitting cells

\-glia: support cells

digestive system: oral cavity

\-ingestion of food

\-initial breakdown of food through mechanical (teeth and tongue) and enzymatic action (salivary glands and saliva begin to break down amylase which breaks down carbohydrates)

digestive system: pharynx and esophagus

\-pharynx (throat) opens to both trachea (leads to lungs) and esophagus (leads to stomach)

\-when breathing sphincter seals off esophagus

\-when swallowing epiglottis seals off trachea

digestive system: stomach

\-function: storage of food, mechanical digestion(churning), chemical digestion (gastric juice)

\-very flexible walls to accommodate changing volumes of food

\-acid: HCl (parietal cells), denatures proteins

\-enzyme(cheif cells): pepsin-a protease

\-simple columnar epithelium specialized for secretion

digestive system: small intestine

\-functions: continued chemical digestion of food assisted by proteins from the pancreas, liver, and gallbladder and absorption of nutrients

\-chemical digestion aided by: amylases (breakdown of carbs), proteases (breakdown of proteins), nucleases (break down of nucleic acids), lipases (breakdown of fats)

\-maximizing absorption by increasing surface area: plicae (circular folds of whole epithelium), villi (finger-like projections of epithelium into lumen), microvilli (thick “brush border” on apical surface of epithelial cells)

digestive system: liver

\-nutrient rich blood from intestines travels to the liver through the hepatic portal vein before being distributed to the rest of the body

\-liver plays an important role in detoxification of blood

digestive system: large intestine

\-functions: some additional digestion of food and nutrient absorption with assistance from gut microbes, absorption of water, production of feces

digestive system: cecum and appendix

\-cecum: pouch used to improve digestion of plant material (not very prominent in humans)

\-appendix: harbors beneficial bacteria and immune cells

digestive system: the colon

\-food moves through due to peristalsis (smooth muscle)

\-time in colon determines amount of water absorbed (more time=more water absorbed leading to constipation and less time=less water absorbed leading to diarrhea)

\-leads to rectum and anus where waste is expelled from body

digestive system: regulation of appetite

\-appetite suppressors: PYY (secreted by small intestine when food is present), Insulin (secreted by pancreas when blood sugar is elevated), Leptin (secreted by adipose tissue)

\-appetite promotor: Ghrelin (secreted when stomach is empty)

pancreas in regulating blood glucose homeostasis

\-set point: 70-110 mg

\-stimuli: above 110 or below 70

\-sensor: detected by pancreas

\-responses: pancreas secretes insulin, liver absorbs insulin and stores it as glycogen

blood glucose disrupted in diabetes

Type 1:

\-autoimmune disorder: your own immune system attacks the pancreatic beta cells

\-as a result the pancreas cannot produce insulin

Type 2:

\-metabolic disorder

\-pancreas still produces insulin but cells throughout the body lose the ability to respond to the insulin

structure and direction of blood flow in the circulatory system

\-right atrium (receives deoxygenated blood), right ventricle, pulmonary arteries, lungs (reoxygenated), left atrium, left ventricle, aorta (takes O2 to body), blood then deoxygenated, vena cava brings deoxygenated blood back to heart

structures in the heart that contribute to heart contractions

\-cardiac muscle: capable of powerful contractions that generate the force necessary to propel blood throughout the body

\-all chambers relaxed as blood flows into atria from veins (diastole)

\-atria contract simultaneously to force blood into relaxed ventricles (atrial systole)

\-ventricles contract simultaneously to force blood into arteries (ventricular systole)

structure and function of arteries

\-transports blood away from the heart (usually deoxygenated) and branches into capillaries

\-blood pressure is highest here

structure and function of capillaries

\-very thin walls for gas/nutrient/waste exchange in tissues of the body and reconverge into veins

\-lower blood pressure here

structure and function of veins

\-transports blood back to the heart (usually oxygenated)

\-blood pressure is lowest here

function of plasma

transports nutrients, transport carbon dioxide and other wastes, clotting and wound healing, protection from pathogens

erythrocytes

\-red blood cells

\-hemoglobin: iron-containing protein that carries oxygen, gives blood its red color

\-red blood cells lack a nucleus which helps them fit through narrow capillaries

leukocytes

\-white blood cells

\-mixture of immune cells which actively fight off infections