general biology test 2

lesson 7 - phylogeny

%%carl linneas 1707-1778%%

created the ==Linnean== system of binomial naming

%%why not use English names%%

latin was the language of the world

mountain lion example - over 50 names for it just in English. even within the us, no one can agree

%%how many living species%%

8.7 million estimated species living

1.2 million identified

1 million insects

350 000 beetles

10 billion species ever estimated

70% of species live in ==biodiversity hotspots==

%%using phylogeny to show relationships%%

==phylogeny== - evolutionary history of species or group of related species

measures relatedness of documented species

discipline of systematics uses phylogeny to classify organisms and determine evolutionary history

uses fossil, genetics, and morphological data to infer evolutionary relationships

%%binomial nomenclature%%

18th century carl Linnaeus published a system based on resemblance

two part names. capitalize genus not species

%%hierarchal classification%%

grouped in increasingly broader categories

kingdom phylum class order family genus species

%%classification method%%

systematicists use phylogenetic trees to learn about evolutionary relationships

==sister taxa== - are groups that share an immediate ancestor

==polytomy== - when the tree is split into more than 2 branches. this shows unclarity in evolutionary history. an unresolved pattern of divergence

common ancestor - LUCA - last universal common ancestor

%%phylogeny can be inferred from morphological and molecular data%%

physical and genetic similarities are called ==homologies==

organisms that look similar are likely closely related

%%applying phylogeny%%

provides important info for characteristics in closely related species

used to infer unknown species by analyzing them w known species

trace evolutionary history

relationships within species

ex corona virus - alpha and beta infect humans but SARS-CoV-2 is not part of either

Lesson 8 - molecular clocks and pandemics

%%DNA as a historical document%%

comparing DNA to infer relatedness is a valuable approach for tracing organisms evolutionary history

your DNA is a historical record of mutations in your lineage

nuclear DNA changes slowly and is useful for investigating branching points many years ago

mitochondrial DNA changes rapidly and can be used to explore recent evolutionary events

so if you want to find out something from a long time ago, use nuclear DNA, recent - mitochondrial DNA

nuclear dna is from mom and dad. mitochondrial is just from mom

%%viral fossils in our DNA may help us fight infections%%

with your DNA you might be able to find out what viruses your ancestors had

bacteria can make itself home in your genome

can also find criminals by DNA testing and matching to parents

%%four types of nucleotides in DNA%%

cytosine and thymine are single ringed pyrimindines

guanine and adenosine are double-ringed purines

a-t c-g chargaffs rules

==transitions== are between a/g and t/c

easier bc same chemical group

==transversions== are between all other

dna gets extracted from organisms the sequenced. this helps when comparing dna to other organisms

dna can be sequenced and aligned to determine similarity and differences in taxa

%%orthologous genes%%

similar genes found in 2 individuals

after sepciation, ==orthologous genes== continue to diverge from one another between 2 individuals

ex. if gene x from a worm and a snake look similar they are orthologous genes

%%paralogous genes%%

==paralogous genes== are result of gene duplication so are found in more than one copy of a single gene in an organisms genome

each gene copy can undergo mutation and can often evolve new functions

%%evolution of genomes%%

orthologous genes are widespread and extend across a variety of species

ex. humans and mice diverged about 65mya yet 70% of our genes are orthologous

gene number and the complexity of the organism are not strongly linked

ex. humans only have 4x more genes than yeast

genes in complex organisms appear to be very versatile and each gene can perform many functions

%%molecular clocks or molecules as clocks%%

uses constant rate of evolution in some organisms to estimate the time of evolutionary change

orthologous - nucleotide changes are proportional to the time since they last shared a common ancestor

paralogous - nucleotide changes are proportional to the time since the genes became duplicated

molecular clocks can change known fossil records

==coprolites== (poop) can be fossilized and studied

%%problems w molecular clocks%%

sometimes does not run as constantly as expected

irregularities result from natural selections and gene flow

estimates evolutionary divergence older than the fossil record have a high degree of uncertainty

%%molecular clock application - the origin of HIV%%

phylogeny shows that it comes from primates (chimps and apes)

spread more than once as shown on tree

==zoonosis== - study of a transfer of a virus from one host to another

application suggest spread to humans about 1930’s

%%molecular clocks to trace zoonosis%%

easy to read is called a clatogram

transfer: airborne, close proximity, food borne (meat/milk), direct contact (bite)

==zoonotic viruses== - viruses that has made the jump from animal to human

tibean plateau, china - epicenter of H5N1 avain flu outbreak in jan 2005

began w 600 migration bird deaths

%%global pandemics%%

H5N1, Zika, and CoVid-19 are viruses

bacteria can experience outbreak too

==methicillian-resistan staphylococcus aureus (MRSA)== is a bacteria that comes in two distinct types and first identified in 1960

all MRSA outbreaks involve the 2 types

their dna sequences have remained unchanged bc they have not received pressure from their environment to undergo natural selection

lesson 9 - bacteria

==blooms== - bacteria spreads rapidly due to sudden favourable conditions

grand prismatic spring - Yellowstone national park

%%prokaryotes: bacteria and archaea%%

first life 3.5 bya (stromatalites)

prokaryotes thrive almost anywhere

most prokaryotes are microscopic therefore extreme conditions have less of an effect on them

==prokaryotes== - first life, no organelles, only nuclear, bag of stuff

==extremophiles== - organisms that love to live in extreme conditions

ex. ==thermophiles== (heat), ==psychrophiles== (cold), ==halophiles== (salt), and ==acidophiles== (acidic)

more prokaryotes in a handful of fertile soil than people ever lived on earth

2 domains - ==bacteria== and ==archaea==

%%bacterial diversity%%

outnumbers all other organisms on earth

land, aquatic, parasitic

==metabolic diversity== allows them to live almost anywhere (different strategies orhanisms have discovered to obtain energy)

10k species identified

smallest is 200nm, largest is 500um

eukaryotes share a more recent common ancestor with archaea than bacteria. archaea and bacteria do not share a common ancestor

%%structure and behaviour of prokaryotes%%

very likely earths first organisms 3.5bya

unicellular

0.5 to 5 um prok - much smaller than the 10 - 100 um euk

prok cells have a variety of shapes

temporary colonies, infections change

^^3 most common shapes^^

==coccus== - spheres

==bacillus== - rods

==spiralis== - spirals

^^diplo-, strepto-, and staphylo-^^

==diplo== - pairs

==strepto== - lines

==staphylo== - chucks

==streptococcus pyogenes== - the causitive bacteria of ==pharyngitis==

==staphylococcus== - staph infection

cell surface detremines bacterial preperty

bacterial walls contain ==peptidoglycan==, a network of sugar polymers cross-linked by amino acid polymers

==gram positive== - simpler walls w larger amount of peptidoglycan, purple

==gram-negative== - less peptidoglycan and an outer membrane, pink

%%gram staining%%

many antibiotics target peptidoglycan and kill it. meaning many antibiotics only work for g pos bacetria. we dont want to kill our own cells by targetting somthing else. only bacteria have peptidoglycan

%%structure of the plasmamembrane%%

certain prokaryotes have specialized membranes that perform metabolic functions

usually infoldings of the plasma membrane

%%prokaryotic dna organization%%

prok has less dna than euk

genome is circular chromosome

some bacteria have rings of dna called ==plasmids== - auxillary dna

%%reproduction and dormancy%%

reproduce by ==binary fission== and can divide every 1-3 hours

many prok form metabolically inactive endospores which survive harsh conditions for centuries

lesson 10 - archaea

proteobacteria - gram neg - largely pathenogenic

gram neg - little peptidoglycan so wont stain and hard to treat.

==ciproflaxin== - drug to kill gram neg. kills all bacteria so youll get more sick before you get better bc killing microbiome (good bacteria)

%%proteobacteria%%

divided into diff categories - alpha, beta, gamma, delta, epsilon

==rhizobium== - lives symbiotically in roots of plants to make soil rich

remember these bacteria!

1. bifidobacterium
2. streptococcus pyogenes
3. heliobacter pylori
4. yersinia pestis

==heliobacter pylori== - inside stomach, causes bleeding, takes months to get rid of, deadly infective

%%black dealth / the plague%%

mice borne (gamma proteobacteria)

==yersinia pestis== - attacks lymph nodes. inactivates your immune system then divides. forms ==buboes== from swollen lymph nodes. has its own sculpture in europe bc it shaped immigration

%%bacteria: the others%%

^^clamidias^^

parasites in animal cells

==chlamidia trachomatis== - causes blindness and inflammation of the urethra, sex transmit

^^spirochetes^^

some are parasites - ==treponema pallidum== (syphilis), ==borrelia burgdorferi== (lyme disease), meningitis

^^cyanobacteria^^

members can photosynthesize

ex. stromatilites, early earth

found in abundance in present earth oceans - 85% of earths photosynthesis

==zoonosis== - jumped to humans

%%archaea%%

anaerobic

methano - flamable

diverged from eukaryotes more recently than bacteria

extremophiles - ==halophiles== (saline), ==thermophiles== (hot), ==nyctophiles== (dark), ==mesophiles== (neutral but still anoxic)

methanogens - produced mathane by archaea, anaerobic respiration. live in swamps and marshes, poisoned by oxygen

in recent years, many new groups of archaea have been identified usung ==meta-genomics== - finding dnas of archaea w/out having to observe their physocal presence

some may offer clues to the evo.ution of early earth and life

%%impact of prokaryotes on humans%%

some prokaryotes are human pathogens and others are positive

^^mutualistic bacteria^^

human intestines are home to many bacteria which help us. 500-1000. established ~ 2 yrs

^^probiotics^^

introducing healthy bacteria into your intestines

ex. ==lactobaccillus== in yogurt

lesson 11 - protista, excavata, alveolata

==gromia== - single cell euk - ocean floor sea grape

%%protista%%

unicellular euk

sexual and asexual reproduction

flagella for mobility

nutritionally diverse

==photoautotrophs== - contain chloroplats (photosynthesis)

==heterotrophs== - ingest larger food and particles

==mixotrophs== - combination

ex. amoeba, paramecium

%%excavata%%

free-living and parasitic

amitochondria or pseudo-mitochondria (modified mito)

(so some have none and some have a makeshift)

have a feeding groove to injest food

include: diplomonad, parabasalid, euglenazoa (euglenid, kinetoplasid)

%%excavata: diplomonad%%

anaerobic

modified mitochondria called ==mitosomes==

2 equal size nucleai

multiple flagella

often parasites

ex. ==giardia intestinalis==

human infestation charchateized by diarrhea and neusea

water borne

%%excavata: parabasalid%%

reduced mito called ==hydrogenosomes== that generate some energy

ex. ==trichomonas vaginalis== - pathogen that causes a type of yeast infection in human females

%%excavata: euglenozoa%%

predatory heterotrophs, photoautotrophs, and parasites

main feature - spiral / crystalline rod of unknown function inside flagella

includes euglenids and kinetoplastids

%%excavata: euglenozoa: euglenid%%

1 or 2 flagella that emerge from a pocket at one end of the cell

mixotrophic

presence indicate high levels of dissolved organic matter

has an eye spot

ex. euglena (saw in lab)

%%excavata: euglenozoa: kinetoplastid%%

organized mass of dna called ==kinetoplast (not a nucleas)==

free-living

heterotrophs

fresh water, marine, moist terrestrial ecosystems

parasitic members like ==trypanosoma== which causes sleeping sickness in humans

==leishmania== - spread by sand flied, causes ==leishmaniasis== - skin sore and comprimised immunity

kinetoplastids evade human response by switching surface proteins

each cell produces millions of copies of a single protein

each new generation produces millions of copies of a different proetin

these frequent changes prevent host from developing immunity

%%alveolata%%

members have membrane bound sacs (alveoli) just under the plasma membrane. fxn is unknown

include: ==dinoflagellates== and ==apicomplexa==

%%alveolata: dinoflagellates%%

2 flagella, each reinforced by cellulose plates

abundant components of both marine and fresh water microbial communities

aquatic photoautotrophs, mixotrophs, and heterotrophs

toxic flagellate blooms

%%alveolata: apicomplexa%%

parasites of humans and animals

complex of organelles at its apex speciallized for penetrating host cells and tissues

require 2 or more diff host species to complete reporductive cycle

ex. ==plasmodium== - causes malaria - requires noth miquitos and humans to complete its cycle

lesson 12 - opisthokonta

==microdosing== - taking small amounts of a drug, not enough to get high, just enough to enhance creativity

mind altering comes from a ==psychodelic== fungi called ==psilocybin== mushrooms (active ingredient)

%%kingdom: opisthokonta%%

includes some ==metazoans== (multicellular basic eukaryotes) and fungi

likely some of earliestmulti cellular eukaryotes ~100mya

greek opisthos (meaning powerful posterior) flagella kontos (meaning pole) to porpell forwards

fungi are closer to anomals than plants

%%basal opisthokonta: slime molds%%

^^plasmodial slime molds^^ form a mass called ==plasmodium==

unicellular w multiple nucleai

undivided by multiple membranes so can have hundreds of nucleai

it extends ==pseudopodia== (fake foot) thorugh decomposing material engulfing food

slime mold makes a sound when growing

when fungi reproduces, it forms a ==sporangium== (like gonads to humans) which is a spore bearing structure

no sperm, flagellated cell and ameoboid cells

^^cellular slime molds^^ form multicellular ==aggregates== (cells separarted my membranes)

feed individually but can aggregate to form multicellular ==fruiting body== to reporoduce

experimental modelfor studying the evolution of multicellularity - no organisms or body axis

plasmodial - sporangium

cellular - fruiting body

honey mushroom - ==armillaria ostoyae==

largest organism on earth

%%fungi%%

essential for terrestrial ecosystems bc they break down organic materials and recycle nutrients

spevialized heterotrophs called ==saprophytes== bc they feed by absorption of decayed organic materials

earliest colonizers of land, formed by mutualistic relationship w early plants

decomposers, mutualistic

nutrition and ecology

use complex enzymes to break dowm many molecules into smaller organic compounds

exibit diverse lfestyles - decomposers, parasites, mutualists

%%structure and function%%

morphology and multicellualr have evolved to consume as much nutrients as possible

consist of a newtwork of branched called ==hyphae==. mass = ==mycelia==

mycelias structure maximized SA to volume ratio

fungal walls contain chitin - long chain of glucose derivatives

%%mycorrhizal fungi%%

mutualists w plant roots

unique structire called ==haustorium== that allow them to penetrate the tissues of their host

deliver ions and nutrients to plants, plants deliver all other nutrients to fungi

all land plants have mycorrhizal partners

%%fungal reporduction%%

^^sexual^^

==plasmogamy== - union of cytoplasm from 2 parent mycelia

==karyogamy== - nuclear fission (takes a while)

lesson 13 - fungi

so many types of fungi! including firefox mushrooms. bioluminescent due to luciferace protein. it can be use to find cancer. a tag.

%%ascomycetes%%

marine, fresh water, and terrestrial habitats

produce spores in sac-like ascus

common: sac fungi

vary in size and complexity

truffles (the mushroom) only grow underground. dont have living sporangiums above. pigs sniff out.

include plant pathogens, decomposers, and symbionts

neurospora crassa - common bread mold

cordyceps

%%ergotism%%

ergot of rye - caused by ascomycete and produces toxins

died in large numbers in middle ages bc of this

characterized by gangrene, nervous spasms, burning sensations, hallucinations, temporary insanity

contain lysergic acid, raw material of LSD

%%basidiomycetes%%

puffballs and shelf fungi

classic club shaped mushrooms

good decompsers of wood

supermarket button mushrooms - ==agaricus==

%%what are lichens%%

symbiotic associations btwn photosynthetic microorganisms and fungi

millions of photosynthetic cells are hald in a mass of ==fungal hyphae==

Photosynthesic component is green algae or cyanobacteria, fungal component is ascomycete

scientific names for lichens bc symbiosis is so complete

algae or cyanobacteria occupy inner layer below the lichen surface

==map lichen== - growing in the arctic and has been identified as some of the longest living organisms or earth

a patch for 8600 yrs