bio 1b organismal

blackman

eukaryotes

• linear, chromosomal DNA

• membrane-enclosed nucleus/organelles (mitochondria, plastids)

prokaryotes

• CIRCULAR chomoesome + plasmids

• NO membrane-enclosed organelles or nucleus.

prokaryotic ways of life

• obtaining energy

• reproducing

• coordinating functions within and between cells

autotrophs

obtain energy by GENERATING THEIR OWN food from inorganic molecules

heterotrophs

consume food produced by OTHER ORGANISMS

chemotrophs

energy comes from CHEMICAL REACTIONS

phototrophs

energy comes from LIGHT

• not all PHOTOAUTOTROPHS do oxygenic photosynthesis

prokaryotes, organism metabolism: it can be … or …

AEROBIC, ANAEROBIC

prokaryotes, how do they reproduce?

ASEXUALLY through binary fission

• DNA generally organized into single, circular chromosome + small circular plasmids

binary fission

single cell splits into two cells after doubling in size

• not same as mitosis (no splitting of nucleus)

plasmids

small, circular, extra chromosomal DNA that replicate independently

archaea

prokaryote

• generally extremophiles with anaerobic metabolisms (w/o O₂)

• found in harsh, anoxic environments w/ extreme salinity or temperature

  • under km of ice or animal guts

• some are chemoautotrophs: thrive around volcanic vents + support deep ocean ecosystems (rich w/ H₂S)

• BOON TO MOLECULAR BIOLOGY

extremophiles

organism able to survive in extreme environments

anoxic

a total lack of oxygen

• anaerobic metabolism occurs w/o O₂

bacteria

prokaryote

• diverse, contains species that live by all nutrition/metabolism

• some PARASITES, some PATHOGENS

• play critical ecological roles as DECOMPOSERS of organic matter, recycling NUTRIENTS in environment as SYMBIONTS in animal guts

symbionts

organism of diff. species that live in close physical association w/ host

• can benefit through mutualism, commensalism, or parasitism

earth lacked … as we know it for the first billion years

LIFE

• until ~3.8 bya, periods of heavy bombardment

• atmosphere rich in N₂, NH₄, CO₂

  • NO OXYGEN YET

life starts in…

THE OCEANS

• first evidence of prokaryotic life in FOSSIL RECORD (~3.5 bya)

• stromatolites. LIKELY photoautotrophs but w/o oxygenic photosynthesis

• contained all other anaerobic modes of life (methanogens giving off methane + water as byproducts of metabolizing CO₂ and H₂)

cyanobacteria

PHOTOAUTOTROPHS that capture light energy through OXYGENIC PHOTOSYNTHESIS

• CO₂ + H₂O → sugar + O₂

  • O₂ oxidizes abundant IRON in oceans, causing to precipitate in large bands

• causes “oxygen revolution”

• EVOLVES ability to NITROGEN-FIX, fertilizing oceans for heterotrophs

oxygen revolution

• poisons oceans with O₂ toxic to anaerobes

• increases level of oxygen in atmospher

  • accumulates ozone, protecting life from UV rays

endosymbiont theory

origin of eukaryotic organelles

• archaea-derived ancestor evolved nucleus

  • → eukaryotes ~1.8by ago

archaea likely engulfed … capable of …

BACTERIAL SYMBIONT, AEROBIC RESPIRATION

• instead of just being digested, the bacteria became a permanent endosymbiont (permanent resident of host)

  • formed mitochondrion, allowing for aerobic respiration

instead of mitochondrion, some got a … as an endsymbiont, forming …

CYANOBACTERIUM, PLASTIDS

evidence for endosymbiosis

• inner membranes of organelle have enzymes and transporters homologous to those in plasma membranes of bacteria

• similar ribosomes to bacteria’s

• orangelles have own DNA on circular chromosomes

  • mimics bacteria genome structure, not eukaryotes

• organelles divide by binary fission like bacteria

fill in the blanks

1. heterotroph, anaerobe

2. heterotroph, aerobe

3. autotroph w/ oxygenic photosynthesis, aerobe

prokaryotic ways of life

• obtaining energy (many ways)

• reproducing (binary fission)

• coordinating functions within & between cells

  • metabolic cross feeding, filamentous chains, biofilms, and quorum sensing

microbiome

all microorganisms found in a given well-defined habitate

• includes bacteria, archaea, fungi, algae, other unicellular eukaryotes

• dynamic and environment-dependent

• can have mutualists, commensals, pathogens

  • interactions among species in microbiome community can determine balance

• if in host, can be important for development/nutrition/health

ways microbiomes establish

HORIZONTAL, VERTICAL

horizontal transmission

acquired from the environment

vertical transmission

passed down from parent to offspring

• germline transmission of intracellular symbionts

• acquisition during passage of birth canal

what % of cells on avg human body belong to microbes?

3/5 (60% or 56%)

microbiomes in human gut are acquired…

both horizontal (environment) and vertical (passed on)

• influences development, changes w/ age and diet

• if one bacterial species takes over (typically after antibiotic treatment), not good for environment bc imbalance

prokaryotic cells can still … even if not multicellular

WORK TOGETHER

examples of prokaryotes working together

• metabolite cross-feeding

• filamentous chains

• biofilm

• quorum sensing

metabolite cross-feeding

interactions btwn bacterial strains

• molecules from metabolism of ONE STRAIN are metabolized again by ANOTHER STRAIN

filamentous chains

some cyanobacteria (ex. anabaena) have cells in chains that differentiate and become heterocysts

• allows spatial separation of nitrogen fixation (anaerobic) from photosynthesis (aerobic)

• formed by binary fission

biofilm

surface coating colony of one or more species of microbes engaging in metabolic cooperation. mats of cells secrete and become stuck in a matrix of polysaccharides/proteins

• stromatolites (is calcified biofilm)

• plaque/tartar in mouth

• the reason why antibiotic resistance exists / drug delivery problems

quorum sensing

if enough of other microbes of same type nearby, density-dependent activity happens

• triggers synchronized group behaviors (ex. biofilm formation, virulence, and bioluminescence)

quorum sensing: how to know if microbe pop. reaches high density?

concentration of secreted autoinducer molecules

for billions of years after the first eukaryotes…

• zero soil, continents are big rocks

• oceans have limited nutrient content

• unicellular eukaryotes in oceans continue to radiate

  • some multicellular euk. arise as early as ~1.3bya

• around 700mya, Earth becomes “snowball earth” twice

• post-thaw and continental landmass breaks cases nutrients to enter ocean (via weathering)

• life plants flag on land only ~500mya, still pretty new

characteristics of fungi

• can be multi or unicellular

  • multi are non-motile + filamentous

  • single filament = hypha (plural hyphae), network of hyphae = mycelium

• chitin-rich cell walls

• heterotrophs that engage in absorptive nutrition by secreting enzymes to digest food externally

• stores carbon as glycogen (like animals)

  • not starch

• life cycle includes spores, single cells capable of growing into adult organism

fungi can break down … that most bacteria can’t

LIGNIN

• resulted in balcony collapse killing 6 ppl bc of dry rot

mycelial networks

• growth is indeterminate: no defined end structure

  • can be huge and ancient

• kinda like swarms of exquisitely sensitive hyphal tips connected by parallel processing into one being

• cytoplasmic streaming: a mechanism to distribute pressure, water, nutrients, organelles, and nuclei

problems to solve for mycelial networks

1. finding nutrition if non-motile

2. direction growth w/o central information processor (brain)

3. moving resources great distances

specialized hyphae

arbuscular mycorrhizal fungi: penetrate root cells and create structures are arbuscules

ectomycorrhizal fungi: forms nets around whole root and cell surfaces, does not enter cells

mycelial applications

mycofabrication: biofabrication process using fungal mycelium to grow sustainable materials

mycoremediation: sustainable, cost-effective form of bioremediation to break down, absorb, or remove environmental contaminants

generalized sexual life cycles

meiosis: production of haploid cells from diploid cell over 2 rounds of cell divison

fertilizatio

n: union of haploid gametes to produce a diploid zygote

fungi sexual life cycle

in fungi, products of meiosis are spores

• cells derived from spores then produce

need terms centered on products made instead of meiosis/mitosis

SPOROGENESIS, GAMETOGENESIS

sporogenesis

process of spore formation

gametogenesis

process of gamete formation

which phase predominates: animals/fungi?

animals: diploid phase

fungi: haploid phase

• haploid phase is predominant and can be multicellular in fungi

• no mitosis after fertilization (no multicellular diploid in fungi)

diplontic life cycle

• mitosis occurs only in diploid, so multicellular in diploid

haplontic life cycle

• mitosis occurs only in haploid, so multicellular in haploid

plant life cycles

meiosis makes haploid spores and fertilization makes zygote

• but both spores and zygotes can undergo mitosis in plants, so haplodiplontic life cycle or alternation of generations

need more terms on what multicellular organism makes what products

GAMETOPHYTE, SPOROPHYTE

gametophyte

haploid oranism producingb gametes by mitosissp

sporophyte

diploid organism that produces spores by meiosis

fungal diversity: 1 or many separate origins of multicellularity? monophyletic or not? solution to spore dispersal?

• as many as 2.2-3.8 million species, only 6% described

• united by chitin-rich cell walls

• diverged from common ancestor w/ animals ~1bya

• multiple separate origins of multicellularity distinct from animals & plants

• with move onto land, remaining groups lost flagellated spores as shift from water- to wind-based spore dispersal

• need new spore dispersal solution: fruiting body

• MONOPHYLETIC

fungi can also … reproduce

ASEXUALLY

• many species can make spores w/o going thru a diploid zygote

examples of asexual reproduction

mucuromycota: mycelium forms sporangia w/ genetically identical spores

unicellular yeasts: haploid cells bud off additional haploid cells

multicellular ascomycetes: strings of spores called conidia form as hyphal tip structures

• only ARBUSCULAR MYCORRHIZAL FUNGI asexually reproduce

fungi as pathogens

mycosis: fungal infection

• human fungal infections rarely lethal except in immunocompromised ppl, but difficult to treat

ophiocordyceps

genus of ascomycetes known as zombie fungi

• behavior induced is very specific to organism

  • ants may crawl to optimal dispersal height before death grip then clamps on leaf vein

• at time of death grip, fungi takes 40% body in jaw muscles

  • can see evidence of death grips in fossil leaves ~48mya

what is algae? what is it NOT?

photosynthetic organisms that are not land plants

• live in aqueous environments

• NOT a monophyletic group

• cyanobacteria is blue green algae

ecological group def

a set of taxa that share common ways of life

• may or may not overlap w/ phylogenetics

• decomposers (prokaryotes or fungi), cushion plants (species in many platn groups evolved this)

what event caused these evolutions in algae?

PRIMARY AND SECONDARY ENDOSYMBIOSIS

• eukaryote enters in permanent association w/ prokaryote in primary endosymbiosis

  • prokaryotes become primary plastids

• new plastids gained after 2ndary endosymbiosis is not due to new cyanobacterium, but evolution of one from primary endosymbiosis

  • called secondary plastids

evidence for 2ndary endosymbiosis

1. number of membranes that surround the plastids in organisms (4 instead of 2, always more than 2)

2. some organisms have relic nucleus

3. if sequence genomes of palstids (circular genome), more similar to plastids of green/red algae rather than cyanobacteria found in environment

   1. indicates that it evolved from algae instead of cyano

cyanobacteria, diatoms, dinoflagellates have what in common?

unicellular ONLY

• ex. phytoplankton

brown, red, and green algae have what in common?

can be unicellular or multicellular

• ex. phytoplankton (uni) or seaweeds (multi)

algae are … contributors to global …

HUGE, NPP

• primarily due to unicellular algae (diatoms, dinoflagelletes, cyanobacteria)

  • important base to aquatic food webs

diatoms

unique cell walls made of silica embedded in organic matrix

• 25% of global npp

• deposits accumulate on ocean floor

  • uplifted fossil deposits are harvested as diatomaceous earth (key pat of toothpaste, metal, water filtration

dinoflagellates

• have two flagella, one spiral (makes them spin)

• DINO = WHIRLING

• some have treansition to heterotrophy, some are mixotrophs that can switch from auto or hetero

  • BAD: can create dinoflag blooms producing toxins

brown algae

marine algae including kelps

• kelps r keystone species of intertidal/deepwater

• can grow 200ft long

red algae

red bc pigments absorb blue light

• can come in diverse colors

• economically important

• includes nori (sushi seaweed)

green algae

closest relatives tro plant kingdom

• very diverse forms (uni/colonial/multi)

• found in fresh/sea water, maybe high elevation snow fields

algae life cycle

left diplontic

middle haplontic

right haplodiplontic

• mitosis occurs twice in haploid phase (after spores develop into gametophytes, after gametes come tgt to fertilize)

terrestrialization… where does soil come from?

ONLY ~500MYA, SOIL, comes from lichens

mycobiont? photobiont?

myco: heterotrophic fungus

• provides moisture, shelter, uv protec, minerals

• secretes acid

photo: phototrophic alga/cyanobacterium

• provides sugars, & fixed nitrogen (only for cyanobac)

lichens

ecological group

• combo of at least 1 heterotrophic fungus (mycobiont) and phototrophic alga/cyanobacterium (photobiont)

• take on form completely distinct from individual growth when together

• MYCOBIONTS/PHOTOBIONTS NOT MONOPHYLETIC

• 20% of fungi lichenize, has evolved many times

• can pair w/ multiple partners (non exclusive associations)

• secrete acids like usnic acid

PIONEER SPECIES, CAN MAKE SOIL BY BOTH PHYSICAL/CHEMICAL WEATHERING

how do lichens reproduce?

TOGETHER & ASEXUALLY

ALONE & SEXUALLY

how do lichens reproduce together & asexually?

fragmentation

soredia: bundle of fungi and algaeh

how do lichens reproduce alone and sexually?

fungi produce their own fruiting body

where did soil initially come from?

probably NOT lichens,

• cyanobacteria, algae crusts? early plants themselves?

key needs for plants

soil, enhanced capacity to get nutrients from soilhow

how did plants get enhaned capacity to get nutrients from soil?

mycorrhizal fungi

• symbioses with fungi that made them able to get into crevices of soil

algal ancestors of land plants emerged from…

FRESH WATER

• both molecular/morph trait support this → shared derived traits involve how cells divide, plasmodesmata (channels between cells), tip-driven, or apical, growth

arbuscular mycorrhizal fung were likely…

PRESENT EARLY AND ESSENTIAL

• observed in early fossils, genes involved in symbiosis are found in genomes of charophytes

benefits of coming ashore

light is unfiltered by water

• more accessible carbon dioxide in air than dissolved in water

challenges of coming ashore

1. staying hydrated (water evaporates quicker)

2. acquiring & distributing water (need a distribution system)

3. building support (w/o water, no buoyancy)

4. fertilization (how will motile gametes meet for reproduction?)

embryophytes

land plants that encompasses basically every plant that we have studied

bryophytes

liverworts, mosses, hornwots

1. “leafy” structures pressed close to moist soil are gametophytes

2. stem-like structure rising up are/has sporophytes (attached and dependent on gametophyte for nutrition, NOT FREE-LIVING)

gametophytes … the bryophyte life cycle

RULE

• start from a spore → makes gametophyte → makes antheridia/archegonia → fertilization → zygote in archegonium → embryo → young sporophyte → sporangium

  • DOES NOT HAVE SPOROPHYLL, only a feature of vascular plants (lycophytes, ferns, gymnosperms, angiosperms)

• has male gametophytes that make antheridia & female gametophytes that make archegonia

  • most moss gametophytes are unisexual and can form either antheridia (male) or archegonia (female)

FIGHT PHIL GIA (NO PHIL FOR NONVASCULAR)

sporophyte (entire structure), sporophyll (specialized leaf that bear sporangia), sporangia (structure producing spores)

how do bryophytes address acquiring/distributing water? (problem 2)

PHYLLIDS (not leaves), RHIZOIDS (not roots)

phyllids

thin leaf-like growths that absorb water thru direct in contact w ground/trapping moisture.

• not leaves

rhizoids

long tubular single cell/filaments that do some water/nutrient uptake, but mainly function to anchor plant

• not roots

• also associated w/ arbuscular mycorrhizal fungi

how do bryophytes address staying hydrated? (problem 1)

solution: make sporophyte/spores more waterproof for airborne life

• new waterproofing (waxy, non-permeable cuticle)

• multicellular sporangia (capsule) that produces spores

  • evolutionary co-option of sporopollenin to make plant spores resistant to harsh weather + capable of wind dispersal

solution: protect gametes and new sporophytes as they form through gametangia

• embryo is zygote that is retained in archegonium, develops within maternal tissue

gametangia

new multicellular protective tissues where gametes form

• there are two types of gametangia

  • antheridia, archegonia

antheridia

gamentagia that produce sperm

archegonia

gametangia that produce eggs