bio midterm #2

Domain eukarya

Eukaryote synapomorphies

1. Nucleus

2. Mitochondrial cellular respiration

3. Membrane-bound organelles

4. Linear Chromosomes

5. Cytoskeleton - cell structure, how cells divide

1. Nucleus

• stores DNA

• site of ribosome subunit assembly

• separated from cytoplasm by double membrane with pores

nuclear membrane: 2 bilayers, covered in pores that surround the nucleus

benefits of nucleus

• separates DNA transcription from translation to proteins

  • allows for transcript processes (better quality control)

  • in bacteria and archaea, transcription & translation occur together

  • post transcription processing: 5 prime cap, splicing mRNA

• the nucleus has diversified in different lineages of eukaryotes, and can be used to distinguish them

evolution of the nucleus

must account for

1. double membrane around nucleus

2. nuclear membrane is continuous w/ endoplasmic reticulum (host to ribosomes for protein synthesis)

3. eukaryotic genome has bacterial & archaean genes

lots of competing hypotheses - infolding hypothesis: membrane folded in on itself to create the envelope around the nucleus & the connecting endoplasmic reticulum

2. Mitochondrial cellular respiration

electron transport chain

3. Membrane bound organelles

• intracellular structures wrapped in membranes

• compartmentalizes cell functions for better specialization

4. Multiple linear chromosomes

• number of chromosomes is species specific

  • humans - 46

  • chimps - 48

  • atlas blue butterfly ~ 450

5. Cytoskeleton

• network of protein fibers that facilitate movement and support the cell, among other functions

  • microtubules, intermediate filaments, microfilaments

many synapomorphies

strong evidence of ancesstry of eukaryotes

Origin of eukaryotes

Current hypothesis

• 3 monophyletic domains

• Eukarya sister to archaea

New evidence provides more support for alternate hypothesis

Asgard archaeans make proteins

• Profilin: actin binding protein, essential for maintaining and restructuring cytoskeleton

• Archaean profilin can interact with eukaryotic cell actin

• Likely origin: an asgard archaean engulfed a bacterium & became 1 organism

Eukaryotic innovations:

1. Endosymbiosis

2. Sexual reproduction - meiosis

3. New feeding modes

4. New locomotion

5. Multicellular

Endosymbiosis is the origin of organelles

• symbiosis - individuals of 2 different species live in physical contact, often for mutual benefit

• endosymbiosis - occurs when an individual of one species lives inside another individual of another species

Endosymbiosis hypothesis

• mitochondria originated from bacterial cell that took up residence inside another cell

• occurred in the ancestor of all eukaryotes

host cell (likely asgardian archaean) → 1. host cell surrounds & engulfs bacterium, 2. bacterium lives within host cell → 3. endosymbiosis: host cell supplies bacterium w/ protection & carbon compounds. bacterium supplies host w/ ATP

Origin of Mitochondria

• double membrane bound organelle

• replicate by fission

• has its own circular DNA

• has its own ribosomes & makes its own proteins

• hosts energy - producing metabolic machinery

• mitochondrial DNA is closely related to a α-proteobacteria

• mitochondrial DNA passed down maternally

Origin of Chloroplasts

• double membrane-bound organelles in plant lineages

• replicate by fission

• has its own DNA

• genome similar to cyanobacteria

• has its own ribosomes and makes its own proteins

Primary Endosymbiosis

1. simple eukaryote + bacterium

2. primary endosymbiosis involves a eukaryote engulfing a prokaryote

3. piece of eukaryote membrane pinched off from eukaryotic cell during endocytosis, bacteria now has 3 membranes separating it from the outside world

Photosynthesis in Eukaryotes

• plantae lineage chloroplasts have double membranes

• other photosynthetic eukaryote chloroplasts have 4+ membranes (b/c secondary endosymbiosis)

Secondary endosymbiosis

• engulfing a eukaryote that has an ancestor that engulfed a prokaryote

  • results in many membranes

• at least 3 separate events spread photosynthesis throughout eukaryote tree

1. eukaryote + eukaryote that contains a chloroplast via primary endosymbiosis → secondary endosymbiosis involves a eukaryote engulfing a eukaryote → bacterium now has 5 membranes separating it from the outside world (1 bacterium’s original membrane, 2 PM gained from primary endosymbiosis, 3 PM of the cell engulfed in secondary endosymbiosis, 4 piece of PM pinched off from engulfing cell in secondary endosymbiosis, 5 eukaryote’s own membrane

Sexual reproduction

• new individuals are formed when gametes (sperm & egg) fuse together

• allows for genetic variation to increase

  • more diversity upon which selection can act

Sex & ploidy level

ploidy level: number of chromosome copies

• haploid = 1 copy

• diploid = 2 copies

• triploid = 3 copies (not common in animals, in flowers, complicates sexual repro)

across domains

• bacteria & archaea are haploid

• eukarya can haploid or more

species’ ploidy level must be maintained generation to generation

Asexual Reproduction in Eukaryotes: mitosis

• like fission in that it results in 2 identical cells

• distinct in that it requires microtubules , which are not present in prokaryotic cells (though some have a similar, but distinct structure

Sex requires the fusion of parental gametes

Meiosis: divides cells chromosome number in half

germ cell w/ 46 chromosomes —meiosis→ egg w/ 23 chromosomes → baby w/ 46 chromosomes

germ cell w/ 46 chromosomes —meiosis→ sperm w/ 23 chromosomes → baby w/ 46 chromosomes

chromosomes —interphase→ homologous chromosomes —meiosis I→ daughter nuclei —meiosis II→ distinct cells

Changing environment hypothesis

during changing conditions, parents with offspring having different genotypes have a better chance of one being successful

Red Queen hypothesis

• increased genetic variation allows for better survival against ever-evolving parasites, pathogens, and predators

• red queen from Alice in Wonderland “we must run just to stay in the same place

Feeding modes: bacteria & archaea

secrete enzymes, absorb simple molecules

Feeding modes: eukaryotes

eukaryotes evolve the ability to ingest whole particles and internally digest (via phagocytosis or feeding grooves)

some eukaryotes can photosynthesize and eat food (mixotrophs)

Locomotion: amoeboid motion

sliding movement observed in some species that is accomplished by cytoplasmic streaming of pseudopodia

• requires ATP

• related to muscle movement in animals

• key immune system cells in humans use amoeboid movement

Locomotion: cilia & flagella

• swimming movement

• flagella: long and found alone or in pairs

• cilia: short & very numerous

multicellularity

• single organisms contain more than 1 cell

• allows for larger size and specialized tissues

• evolved at least 10 different times in eukaryotes

  • animals (1), fungi (3), algae (6)

Eukaryote diversity

1. cellular diversity

• support structures

• flagellum number and appearance

• metabolism

2. life cycles

Cellular diversity: support structures (cell walls)

• silica - glass

• cellulose

• calcium carbonate

Cellular diversity: support structures (internal support)

• alveoli - air sacs in lungs

• pellicles - protein strips

• cytoskeleton

Cellular diversity: flagella

• some lineages have 2 flagella, some have 1 flagellum

  • some have none

• one group is defined by having 2 flagella and 1 has hair like projections on it

Cellular diversity: metabolism

• one clade lost their mitochondria, but have mitochondria like genes in the nucleus

  • live in low oxygen environments → costly to maintain mitochondria in low O2

• bioluminescence

(not on test) Life cycles

diplontic: multicellular stage of life is diploid

haplontic: multicellular stage is haploid

alternation of generations:

• alternate between faces

• multicellular haploid stage, multicellular diploid stage

Ecological importance

• diatoms alone fix 20-25% of all carbon

• diatoms - cycling silica, calcium

Medical importance

• eukaryotic disease has shaped human evolution

• even w/ modern medicine, they can be much more difficult to combat because eukaryotic cells are more similar to our cells than bacteria are

  • drugs that combat eukaryotic cells cause horrible side effects

• often spread by an insect vector

Toxoplasmosis (toxoplasma gondii)

• cats are definitive host, but humans become infected by eating food contaminated w/ ocysts in cat feces

• major danger is to unborn, immunocompromised

• vector - cyst in cat poop not insects

• symptoms - cysts internally in muscles, brain (problems)

Red Tides

• overgrowth of dinoflagellates

• can deplete dissolved oxygen, killing local marine life

• produce neurotoxins that contaminate shellfish

• vector - consuming contaminated shellfish b/c of rd tide

• symptoms - food poisoning, then neuro - numbness in limbs, face, inability to speak properly

Alveolata: Malaria (plasmodium)

location of bite - bit, then they spit in the wound → malaria cells travel to the liver, those cells get big & pop, then they enter the blood stream and more cells/RBC pop, bit by another, mosquitos repro

bite & spit → malaria travels to live → repro in liver & pop → infects RBC → biten again by another mosquito, that mosquito now has malaria

• symptoms - lethargy, sweat, aching body/pain, symptoms of anemia in severe cases b/c RBC burst

• healthy adult → sucks but will feel better, 5 and under = fatal, new vaccine

• malaria & sickle cell trait

Giardia

• found in freshwater, especially at high altitudes

• major GI tract symptoms - diarria, etc., might feel better & come back if 1 stays in intestinal tract

• eukaryotes, requires anti eukaryote antibiotics

Brain Eating Amoeba - Naegleria Fowleria

• live in freshwater in warm areas (warmer water)

• not dangerous if ingested, but bad if you get it up your nose

• up nose/sinuses → forms cysts in brain and eats it

• 179 cases in U.S. since 1950, 4 survivors

• no treatment

• cognitive delays, then death immediately, 2-7 days

African Sleeping Sickness

• spread via Tsetsefly bites

• early stage: fever, headaches, joint pain

• later stage: neurological symptoms, coma, death

Chagus Disease

• spread by kissing bugs

• bite multiple times, excrete, if they have chagus causing eukaryote it gets into the bite wound

• early stage: flu like symptoms, swelling of lips or eyes (bite location) then most recover fully

• chronic phase: heart infection up to 30 years after bite (only in ~30% of people get this phase), chagus in heart

• chagus disease now endemic to California

Leishmaniasis

• spread via sandfly bites

• bite → injects leish → your body sends WBC → leish infects the WBC → reproduces → body sends more WBC → leish keeps infecting WBC and reproducing

• caused by trypanosome type organisms in the leishmania genus

• 3 types

  • 1. cutaneous - skin only

  • 2. viceral - liver, life threatening

  • 3. mucocutaneous - skin, mucus membranes (face)

    • basically dissolves mucus membranes

• medicine, but so bad for liver that it almost kills your liver

• terror is a side effect, they scream

Animal Characteristics

1. Multicellular

2. Extracellular matrix made of collagen

3. Heterotrophic

4. Movement

5. Most are diploid with haploid gametes

6. Develop via a blastula

2. Extracellular matrix made of collagen

• collagen is an elastic connective tissue

• present in skin, muscles, cartilage, & bones

• ones of the most common proteins in animal body

• (ex. scurvy, lack vitamin C, vit C is important in collagen production)

3. Feeders (heterotrophs)

• Suspension feeders

• Fluid feeders

• Deposit feeders

• Mass feeders

Suspension feeders

capture food by filtering out particles floating in water or drifting through the air

Fluid feeders

suck up or mop up liquids like nectar, plant sap, blood, fruit juice

Deposit feeders

ingest organic material that has been deposited within a substrate or on its surface

Mass feeders

take chunks of food into their mouths

Ecological roles:

Detritivores: feed on dead organic material

Herbivores: feed on plants or algae

Carnivores: feed on animals

Omnivores: feed on a combination of plants, animals, fungi, protists, archaea, and/or bacteria

4. Movement

• find food or mates

• escape from predators

• disperse to new habitats

• all animals (except sponges) have muscle and nervous tissue

Metamorphosis

massive morphological change occurs between juvenile & adult life cycle stage

• avoid competition between juveniles and adults

• allow movement for species that are sessile as adults

Early embryonic development: zygote → blastula

• blastula is a hollow ball of cells

• blastula development allows for differentiation of tissues

Animal Categorization

1. body symmetry

2. tissue layers

3. gut type

4. body cavity type

5. nervous system organization & cephalization

(1) Animal Categorization: body symmetry

• bilateral: single plane of symmetry

• radial: multiple planes of symmetry

• asymmetry: no plane of symmetry

• pentaradial: 5 planes of symmetry

(2) Animal Categorization: tissue layers

tissue layers

• endoderm: internal tissue lining (gut)

• mesoderm: musculature, lining of body cavity

• ectoderm: external layers (epidermis)

tissue layer organization

• no tissue layers (porifera only)

• diploblastic: 2 layers (endo & ecto)

• triploblastic: all 3 derm layers

tissue differentiation

• gastrulation

  • formation of the gastrula

  • infolding of the blastula

  • placement of cell within gastrula determines tissue’s fate

• building the animal’s digestive tract

tissue layers

• endoderm: internal tissue lining (gut)

• mesoderm: musculature, lining of body cavity

• ectoderm: external layers (epidermis)

tissue layer organization

• no tissue layers (porifera only)

• diploblastic: 2 layers (endo & ecto)

• triploblastic: all 3 derm layers

tissue differentiation

• gastrulation

  • formation of the gastrula

  • infolding of the blastula

  • placement of cell within gastrula determines tissue’s fate

• building the animal’s digestive tract

Gastrula

(review diagrams)

ectoderm: outer surface → epidermal cells of skin, central nervous system → neuron of brain, neural crest → pigment cell (melanocyte)

mesoderm: dorsal → nodochord, paraxial → bony tissue, intermediate → tubule cell of the kidney, lateral → red blood cells, head → facial muscle

endoderm: digestive tube → stomach cell, pharynx → thyroid cell, respiratory tube → lung cell (alveolar cell)

germ cells: male → sperm, female → egg

(3) Animal Categorization: gut type

two way/blind/incomplete gut:

• one opening

  • animal eats & excretes via same orifice

• food moves in 2 directions

one way/complete gut

• two openings

  • animals eats w/ mouth, excretes w/ anus

• food moves in 1 direction

processing gut:

• one way gut w/ specialized regions that perform different tasks

  • humans have a processing gut

  • annelida

(4) Animal Categorization: body cavity type

coelom

• hollow body cavity that is completely lined w/ mesoderm

• provides a space for oxygen and nutrients to circulate

• enables internal organs to move independently of each other

acoelomate

• tribloblastic organisms that do not have a coelom

coelomate:

• triploblastic organisms that do have a coelom

pseudocoelomate:

• triploblastic organisms that have a hollow body cavity, but it is not completely lined with mesoderm

(5) Animal Categorization: nervous system organization & cephalization

evolution of the nervous system

• early: diffuse nerve net

• late: central nervous system (brain w/ connected nerve system)

cephalization

• concentration of nervous & sensory tissue at 1 end of the body (ex. having a head)

• coincided with the evolution of a central nervous system (CNS)

• bilaterally symmetrical organisms

  • bilaterial symmetry & cephalization go together b/c:

    • this type of symmetry implies directionality of movement

    • move forward through your environment - having all your sensory organs go first so you can see/feel/smell/taste where you are going

  • diversification of sensory organs

    • sight stimulus - light

    • taste stimulus - molecules

    • hearing stimulus - sound

    • touch stimulus - contact, pressure

Causes of Animal Diversification (what caused the cambrian explosion)

1. high oxygen levels in atmosphere at start of cambrian explosion

• aerobic respiration

2. more food availability leads to more feeding strategies

• some will be predatory strategies, leading to #3

3. predation feeding strategies leads to evolution of protective structures, rapid movement, sensory organs in prey animals

4. new niches lead to more new niches

• once animals could move off ocean floor, they can exploit new resources

• this expansion continues leading to predators, symbionts, etc.

5. evolution of “genetic toolkit”

• various sets of developmental regulatory genes allow for huge changes to body organization, without major changes to genome

Developmental Regulatory Genes

• genes that activate protein coding genes early in development

  • tell protein coding genes where to build body parts, but not how to build body parts

Hox Genes

• virtually no variation within a species because all members of one species want bodies arranged in same manner

• highly conserved between species too

  • ex. all vertebrates want head, torso, and limbs in roughly the same spots

• differences only occur at levels telling embryo how

Deep/Genetic Homology

• similar structures evolved in different animal groups independently (homoplasy)

• the genes used to produce these structures evolved very early in animal evolution (homology)

  • sponges have genes that make muscles

  • jellyfish have genes that could make them bilaterally symmetrical

  • → if gene is turned off & no proteins are made, you don’t get the muscles or bilateral symmetry

Animal Diversification key points:

1. animal evolution is more complicated than ‘simple to complex’

2. key innovations did not all arise at once

3. evolution is still occurring within every lineage of animals

Choanoflagellates (outgroup to animals)

outgroup to animals

• sessile; can be solitary or colonial

• cells have a “collar”

• filter feed with collar

Choanoflagellates → Porifera

sponges are choanoflagellates that became multicellular instead of a colony

Phylum Porifera

• fossils from 700 MYA

• no true tissues, organs, or symmetry

• synapomorphies (always find in sponges)

  • choanocytes w/ flagella

  • spicules

Spicules

• support & defend the sponge’s body

• made of calcium or silica

• the structure & shape can be used as a taxonomic feature

Sponge body plan

• Spongocoel - cavity in sponge

• osculum - top of sponge

• choanocytes - inner layer

• inner layer choanocytes

• outer layer is dead tissue

  • contains collagen & spicules

  • holds sponge together

  • some lining cells can be found there

After Poriferans, animals develop true tissues

Cnidaria & Ctenophora are radially symmetrical

Phylum Ctenophora:

comb jellies

• use sticky (but not stinging) cells called colloblasts to catch prey

• named for their cilia, which they use to move

• independently evolved a complete gut, primitive CNS, & mesoderm muscles (in some groups)

ctenophore’s position on the tree of life is debated:

ctenophores possess:

• an integrated nervous system & a primative CNS

  • cnidarians only have a nerve net

• mesoderm muscles

Phylum Cnidaria:

sea jellies, corals, anemones

• 2 way gut

• nerve net

• medusa body form

  • swimming

• polyp body form

  • sessile

Cnidocytes: stinging cells

• nemotocytes are the stinging organelle inside the cnidocyte

• spear hits you, imbeds, injects venom

Class Anthrozoa (phylum cnidaria)

• coral & anemones

• do not display the medusa form (polyps only)

• some corals can reproduce asexually by fission - break off a piece of one color and it will differentiate its tissues into a new individual (useful after hurricanes)

• most corals feed on plankton, yet they live in areas with really low plankton density

  • endosymbiosis of a photosynthetic eukaryote (dinoflagellete) = tertiary endosymbiosis

Class Scyphozoa (phylum cnidaria)

• “jellyfish”

  • can be up to 2 meters wide with 36 meter long tentacles

• asexual reproduction via strobilation/budding

  • one fertilization event can make dozens of individuals

Class Cubozoa (phylum cnidaria)

• box jellies - medusa has a squarer head

• have eyes & can swim much faster than scyphozoans (have muscles to swim)

• stings are incredibly dangerous - can lead to cardiac arrest & death

Class Hydrozoa (phylum cnidaria)

• diverse morphologies & lifestyles, portuguese man-o-war

• often require a colony of conspecifics

  • portuguese man-o-war live in free-floating colonies of medusas & polyps

• less active swimming, more at the mercy of currents

(ctenophores do not equal cnidarians b/c: ctenophores are not radially symmetrical, they don’t have stinging cells, they are not found in open water, they have cilia)

Bilateria

all animals except sponges, cnidarians, & ctenophores

Bilaterian characters

• bilateral symmetry

• 3 tissue layers

• coelom

• complete gut

2 major bilaterian groups:

protostomes & deuterostomes

• differentiated via characters in early embryonic development

  • fate of the blastopore

  • early cell cleavage patterns

  • cell fate determination

Fate of the Blastopore

• protostome - mouth

• deuterostome - anus

Early cell cleavage patterns

a. Spiral cleavage, Lophotrochozoans protostomes

b. Radial cleavage, Deuterostomes

Cell fate determination: protostomes use determinate cleavage

• asymmetrical distribution of cytoplasm between daughter cells means that the body part each cell will become is determined at very beginning of development (ex. after a few mitotic events)

• removing one cell kills the embryo

• aka Mosaic Cleavage

Cell fate determination: deuterostomes use indeterminate cleavage

• symmetrical distribution of cytoplasm between daughter cells means that the body part each cell will become is not determined pre-blastula

• splitting embryo results in twins

• aka Regulative Cleavage

Ecdysozoans

• ecdysis: the process of molting a hard exoskeleton or cuticle

Phylum Nematoda

• round worm

• pseudocoelomates

• differentiated by mouth parts and/or molecular characters

• may be free-living or parasitic

Parasitic Nematodes

Elephantiasis

• condition caused by several different species of nematode

• symptom arises due to nematodes clogging lymphatic system, swollen limbs

• causes: could eat something, step on something (soil), not washing hands

Hook Worm

• intestinal parasite that drinks blood

• causes: contract by walking barefoot outside and have larvae penetrate skin on foot. larvae travel through blood to face and then you swallow the larvae

Pin Worm

• intestinal parasite

• lay eggs in anus of host, fecal transfer to mouths of new hosts

  • 20% of children in USA have pin worms