bio exam 3!!

classification system

• carl von linne; based on anatomical similarities and differences

• the levels don’t show evolutionary relationship

inadequate

the levels do not mean anything

class

mammalia, fish, amphibia, reptile, aves

genus

the only one that is capitalized

species concept

models that define species

the species concepts:

1. morphology species concept

2. biological species concept

3. ecological species concept

4. phylogenetic species concept

morphology species concept

• based on anatomical similarities and differences

• earliest species concept; developed by carl von linne

• pro: always used to classify fossil species

• con: unclear which traits are most appropriate to use as a determining factor ; unclear how much variation justifies naming a a new species

biological species concept

• most commonly used today

• if two organisms can produce viable, fertile offspring, they’re the same species

• pro: great for classifying animals which are restricted in their ability to hybridize

• con: not great for other orgs like plant and bacteria, which are less restricted in their ability to hybrdize.

• results in artificial reduction diversity

new species arise through..

1. reproductive isolation

2. genetic divergence

reproductive isolation

two segments of a population aren’t interacting

genetic divergence

gene pools change, accumulate different mutations until 2 populations (segments) don’t recognize each other

how does reproductive isolation occur?

1. mechanical isolation

2. temporal isolation

3. behavioral isolation

4. ecological isolation

5. gamete mortality

mechanical isolation

• reproductive parts don’t work together anymore.

• ex: pollen won’t stick to stigma and plants

temporal isolation

different breeding season

behavioral isolation

different in the courtship ritual

ecological isolation

different niches

gamete mortality

gametes can’t survive long enough for fertilization to occur

prezygotic barrier

prevents fertilization from occurring

postzygotic barriers

fertilization occurs but offspring don’t meet the criteria

two types of postzygotic barriers

1. reduced hybrid fertility

2. hybrid breakdown

reduced hybrid fertility

offspring are viable, but sterile

hybrid breakdown

offspring are viable and fertile, but the second generation are sick and die

geographic features that may cause reproductive isolation

1. allopatric speciation

2. sympatric speciation

allopatric speciation

a geographic feature splits a population into 2

sympatric speciation

• no geographic barrier

• ex: prezygotic barriers

ecological species concept

• based on habitat/niche.

• pro: makes up for shortcoming in biological species concept.

• Con: due to subtle variation in niche/habitat, artificial increase in diversity

phylogenetic species concept

• based on gene sequence

• pro: makes up for short coming in Bio species concept and removes human bias

• con: how much variation required to justify naming a new species

adaptive radiation

• always follows mass extinction

• a period of rapid change as the survivors adapt to and move into vacant niches

cupsid

• a protein shell

• inside the cupsid; a nucleic acid (DNA or RNA)

cupsomere

individual protein

virsus

• every tissue and every organism on the planet has at least one virus that targets it

• tend to be extremely specific

• its very unusual for them to jump from species to species

capsid shapes

• icosahedral

• helical

• complex

bacteriaphage

• viruses that target bacteria

• most of which we know about viruses comes from studying phages

all viruses that target animals must have an…

envelope

the envelope is derived from the host…

cell membrane

• it has spike proteins embedded in it

• the spike proteins of viral origin and are the only thing that can alert the immune system to the presence of the virus.

naked virus

• standard type of virus

• currently considered non living

• classified obligate parasites

• cannot carry out metabolic process (reproduce) outside of a host cell

lytic life cycle

1. infection- virus inserts nucleic acid into host cell

2. circularization- viral nucleic acid forms a circle to mimic host cell DNA

3. hostile takeover- viral nucleic acid destroys

4. synthesis- new virus assembled

5. lyses- the host cell breaks open and releases the new viruses which targets neighboring cells

inorganic cycle

1. Infection- virus insects nucleic acid into host cell

2. circulization- viral nucleic acid forms a circle to mimic host cell DNA

3. insertion- the viral nucleic acid intergrates itself into the host cell chromosome

*prophage

• can remain there indefinately

• the host cell continues functioning normally

*everytime the host cell undergoes cell division, it produces daughter cells carrying prophage

4. excision- some environmental cue will cause the prohage to remove itself and resume the lytic cycle

5. hostile takeover- viral nucleic acid destroys hosts cell DNA and takes over ribosomes

6. synthesis- new viruses assembled

7. lysis- the host cell breaks open and releases the new virus which targets neighboring cells

classification of animal viruses

1. virulent

2. persistent

3. latent

4. oncavirus

virulent

the classical lytic virus

• ex: the common cold , flu

persistent

chronic replication without killing host cell; like lysogenic but the provirus, will be active, building new virus @chronic low rate; they “bud” out of the host cell without damaging it

• ex: AIDS and hepatitis

latent

virus lies dormant for many years and “hides” usually inside neurons, a stressor activates the virus causing a “flare-up”

• ex: varicella zoster and herpessimplex and shingles

oncavirus

like lysogenic, many cause cancer; each virus can only integrate its DNA into the host cell chromosomes at a specific sequence, if this sequence is found in a gene that regulates cell division, then that virus may “cause” cancer

• ex: papillomavirus

vaccines

prepare the immune system for a specific pathogen

types of vaccines

1. live/attenuated

2. inactivated

3. subunit

4. toxola

live/attenuated

expose the immune system to a living organism

• living; but a less pathogenic relative to a pathogen

• attenuated; a weakened strain of a pathogen

inactivated

radiate a pathogen or otherwise chemically treat a pathogen so that it is no longer virulant

subunit

only expose the immune system to the recognition factor of a pathogen

virus- spike protein

bacterium- external cell wall factor

toxola

doesn’t target the pathogen, but targets a toxin made by the pathogen

big bang

13.7 BYA

the mass in the universe compressed into a mass the size of a dime- the singularity

• the mass “exploded”

• particles like photons and quarks came directly out of big bang

• some elements naturally and spontaneously form: hydrogen, helium, and lithium

photons

particles of light

quarks

exist in groups of 3= hadrons

• protons- 2 up quarks & 1 down quark

• neutrons- 2 down quarks & 1 up quark

• leptons : includes electrons

stars

• big clouds of hydrogen collapse to form stars

• stars live for millions/billions of years

• when they die, the explode, generating the rest of the elements.

• dust may form planets

the big bang: the evidence

1. hubble expansion

2. abundance of H, He, & Li in the observable universe

3. presence of cosmic microwavable radiation

hubble expansion

• the galaxies are moving away from each other

• common point of where galaxies are expanding from

presence of cosmic microwave radiation

energy from the Big Bang in space

is it the only theory?

yes

formation of the earth

4.6 billion years ago

precambrian

• 4.6 BYA- 500 MYA

• the early earth atmosphere came from volcanic outgasing

• the gases contain most of the elements we associate with life- NO, O2, ozone layer…

can these elements recombine spontaneously and abiotically to form organic precursor molecules?

• ex: amino acids, glucose, neucleotides

• scientists look at meteorites, which serve as windows into what exactly earth was like

• scientists finds amino acids and other molecules inside meteorites

• miller tries to spontaneously and abiotically produce organic precursor molecules under stimulated early earth conditions

• experts support the hypothesis that OPM can form spontaneously and abiotically under early earth conditions

can these OPM spontaneously and abiotically form large organic molecules?

• ex: amino acids to protein; neucelotides to DNA/RNA

• lab experiments says: yes

which came first? DNA or RNA

• prob RNA

• DNA probably couldn’t survive in early earth conditions

• RNA can

• - S&A reproduce itself- “reproduction”

• - act as an enzyme- “niche”

• can be favored by selection

• the precursor of life was probably an RNA inside of a membrane

• the *protobiont*

three domains

1. eukarya

2. bacteria

3. archaea

eukarya

• eukaryotic cell type (nucleus and internal membrane system)

• both single and multicellular organisms

bacteria

• prokaryotic cell type (no nucleus or internal membrane system)

• single cell only; include some pathogens

• “germs” strep, staph

archaea

• prokaryotic, but cell has different structure

• especially adaptations for extreme environments

• "extremophiles”

• genetically more similar to eukarya than to bacteria

origin of cells- earliest traces of life

• 3.8 BYA

• isoprenoid residues

• it makes sense that the earliest life would be similar to the archaeans, having features to accommodate extreme features

• we think early earth oceans were similar to hydrothermal vents (very hot and very acidic); archaeans live there today

isoprenoid residues

a membrane component made by archaeans

actual fossils of cells

3.5 BYA

• cyanobacteria

• stromatolite

• banded iron formation

cyanobacteria

• photosynthesis-produces pure o2 gas as a byproduct

• credited with converting the early earth atmosphere to the o2 rich atmosphere as we know it

stromatolites

fossilized mats of cyanobacteria

banded iron formation

• rock containing iron that shows bands of rust as a result of cyclical saturation of the ocean atmosphere w/o2

important outcomes due to the presence of o2

1. no more spontaneous and abiotically producing of biological molecules: o2 breaks things down

2. mass extinction of anaerobic life: anaerobes forced into anaerobic refuges (hydrothermal vents); adaptive radiation of organisms that can tolerate o2

3. ozone layer develops: life can move onto land

orgin of cells

• eukaryote

• 1.9 BYA- single celled

• snowball earth effect

snowball earth effect

• 700 MYA

• global glaciation

• life forced into warm refuges

• may have led to the adaptive radiation of multicellular eukaryotic forms

global glaciation

mass extinction

precambrian ends

• 500 MYA w/ cambrian expansion

• sudden appearance of many recognizable multicellular euk in the fossil record

• all major animal phyla have a represented fossil in the cambrian expansion

paleozoic period

• starts 500 MYA w/ cambrian explosion

• age of giant ferns

• warm and humid climate

• earliest known terrestrial animal (giant millipede)

• age of fishes

• age of giant salamanders- earliest terrestrial predator

• appearance of gymnosperms

• appearance of the ancestor of reptiles and mammals

• appearance of mammal lineage and reptile lineage

• ends 250 MYA w/ permian mass extinction

permian mass extincton

• largest mass extinction

• destroying 90% + of higher taxa on the earth; associated with the formation of pangaea- loss of shoreline (vulcanism)

mesozoic

• starts 250 MYA w/formation of pangaea

• hot and dry climate

• age of reptiles (especially dinosaurs)

• appearance and divergence of birds

• appearance of true mammals (but oppressed by dinosaurs)

• age of gymnosperms

• ends 65 MYA w/ K-T mass extinction

K-T mass extinction

• associated with meteor strike

• destroyed 65% of higher taxa including dinosaurs and birds

cenozoic

• starts 65 MYA w/ K-T mass extinction

• cold and dry climate

• age of mammals

• age of angiosperms

• age of birds- second diversification of birds

• ends w present

fungi main body

• mycelium

• haploid

• coencytic

mycelium

• an interwoven mat of filaments (hypnae); embedded in a matrix (ground, rotten log)

• the “mushroom” is a reproductive structure called a “fruiting body” (produces spores)

haploid

one set of DNA

coencytic

incomplete septum between cells; cytoplasms of adjacent cells run together

four major phyla

1. chytridiomycota

2. zygomycote

3. ascomycote

4. basidiomycota

chytridiomycota

fully aquatic; the most ancient group, most similar to what the ancestor of fungi was like; important parasite of fish and amphibians sign of ecosystem decline

zygomycote

bread mold

ascomycote

implicated in white noise: syndrome in birds

basidiomycota

the one we eat commercially ;characterized by gills

mold

a fungus thats somewhere you don’t want it to be

yeast

• single celled= no mycellium

• saccharomyces

saccharomyces

fermentation and make bread rise

lichens

• symbiotic association of fungis and photosynthetic partner (algae or bacteria)

• obligate mutualists

obligate mutualists

can’t be separated ,together one species

mycorrhizae

• symbiotic association of fungus and plants roots

• 95% + of all vascular plants have a fungus partner

chytrids

• oldest lineage of fungi; suggest evolved from aquatic ancestor

fungi

• cell walls made of chitin

• more closely related to animals than to other kingdoms