BIOL 211 Exam 1

Classification

KPCOFGS: the order of biological groupings/categories

• Kingdom Phylum Class Order Family Genus Species

• To remember: “Keep Pots Clean Or Family Gets Sick”

binomial nomenclature: 2 part scientific name for species

• ex: leopard = panthera pardus

• goes from species all the way down to animal kingdom

• helps in narrowing down by organizing in a concentric way

Phylogenetic Trees

the closer that 2 things = closer ancestry (have more in common)

What phylogenetic trees DO NOT tell us

• order that it appears in does not represent sequence of evolution

• does not represent phenotypic similarity (close related doesn’t mean looking similar)

• don’t tell age

• some branches are proportionate to time but not always

Homology/homologous structures

trees can be built based off these structures and features (only thing that can be used to build trees)

ex: forelimb bones in mammals

Analogy/analogous structures

similarities that appear in unrelated organisms

similar structure/function but different origins

*try to avoid this when building trees

convergent evolution due to similar environmental pressures and natural selection

Cladistics

use homologous structures to place organisms into clades

clade = ancestral group and its descendants

Monophyletic group

Paraphyletic group

Polyphyletic group

Monophyletic group (clade)

ancestral species and all descendants, no group excluded

includes all descendants (single group of animals that are all related)

Paraphyletic group

ancestral species and not all descendants

missing 1 creature from monophyletic group (excluding them)

ex: whale most closely related to hippo but share nothing else in common (terrestrial vs. sea) so they may be excluded since they are so different in other ways

Polyphyletic group

distantly related species and does not include all common ancestors

extra lineage (unrelated family member) distantly related

might use if both inhabit same habitat but unrelated lineage

Shared characters

shared ancestral character = originated in ancestor of clade (biologically in their gene)

• ex: backbone in vertebrates

  • lamprey, bass, frog, turtle, leopard

    • have jaws: bass, frog, turtle, leopard

      • four limbs: frog, turtle, leopard

        • amnion: turtle, leopard

shared derived character = unique to a clade

Central Questions/Key Points For Tree of Life

What is the proper classification order from Kingdom to species and what mnemonic device do you use?

Provide a written example/description of homologous and analogous

Draw out a phylogenetic tree and circle a monophyletic, paraphyletic and polyphyletic grouping on the tree

Provide a written example/description of a shared and derived character

What are the 3 domains in life?

Early Earth

3.8 billion years ago it was mostly volcanic (conditions of Earth were very bad)

eventually the ocean allowed for the first signs of life (it’s where life must’ve first developed)

only prokaryotes existed for 2 billion years

3 domains of life

Archaea and bacteria and eukarya (archaea and bacteria are both prokaryotes)

eukarya and archaea are more closely related than eukarya and bacteria

Prokaryotes Traits

single celled organisms (most are unicellular)

make up bacteria and archaea domains

adapt to diverse and extreme environments

most abundant organisms on Earth

no membrane-bound organelles or nucleus (but still has membranes to perform functions)

first organisms to inhabit Earth

0.5 - 5 um diameter (some are big)

less DNA: circular chromosomes, slightly different RNA code, ribosomes are different from eukaryotes

3 common shapes: spherical, rod shapes, spiral

Prokaryote Movement

Taxis = move towards or away from stimuli (Ex: oxygen, nutrients, chemicals, toxins)

• there is positive and negative taxis (towards = positive, negative = away)

commonly move with flagella (has motor-like function)

• very different from flagella found in eukaryotes

• also different from flagella between bacteria and archaea (ex: different structural proteins)

• flagella = analogous structures between different domains

Prokaryote reproductions

common way is binary fission where it photocopies itself

happens rapidly

short generation time and rapid reproductions which then leads to mutations and genetic diversity

*the key to evolution lies in diversity

Genetic Recombination

transformation = uptake of foreign DNA from surroundings (prokaryote spits out/releases DNA into surroundings)

• limitation: DNA can degrade

transduction = viruses carry genes from one host cell to another (allows for lateral gene transfer)

• limitation: host cell sacrifice

conjugation = DNA transferred between 2 cells that are temporarily joined where they can transfer antibiotic resistance

• MOST EFFICIENT

Prokaryotes and acquiring energy

Energy source:

• chemotroph: obtain energy from chemicals (it must be ingested)

• phototroph: obtain energy from light

Carbon source:

• heterotroph: obtain energy from other organic compounds

• autotroph: obtain energy from CO₂ or related compounds

humans are chemoheterotrophs

-troph = nourishment, chemo = chemical, auto = self, hetero = another

Why prokaryotes can have huge populations and live in diverse envir.

small size and rapid reproduction

mutations

diverse adaptations

rapid evolution (some can have a protective coat)

endospore = resistant cell that can enable bacterium to survive harsh conditions

ex: salt can kill bacteria but not spores

Bacteria traits

most are beneficial but some can cause disease in humans

most live in moderate conditions, some can live in extreme environments

can be producers, decomposers or parasites

cell wall made of peptidoglycan which helps them stay protected (identifying characteristic)

• for eukaryotes cell walls are composed of cellulose or chitin

Classification of bacteria

can be classified according to differences in cell wall composition

• staining a bacteria culture

gram-positive: simple walls, thick peptidoglycan layer (absorbs surrounding materials even toxins), 1 membrane so peptidoglycan just stacks up, creates a thick staining, easier to kill, develops resistance slower

• ex: strep

gram-negative: less peptidoglycan, double membrane, creates a thin stain, hard to kill and quick to develop resistance, thin peptidoglycan layer is covered by membranes that eject toxins

• ex: e. coli

Archaea traits

can be beneficial, not known to cause disease in humans or be detrimental

most live in extreme environments (extremophiles)

no peptidoglycan in their cell wall

were recognized as a major domain in the late 70’s

extreme halophiles: live in highly saline/salty environments

extreme thermophiles: live in very hot environments, adaptations that make DNA and proteins stable at high temperatures

methanogens: live in more moderate environments, release methane gas as they use CO₂ to oxidize H₂ to produce energy

extreme acidophiles: love acidic conditions

extreme psychrophiles: loves the cold

Prokaryote roles: chemical recycling

decomposers - break down dead organisms and waste products

• recycle carbon, nitrogen and other elements

convert molecules into forms that can be taken up by other organisms

fix atmospheric N₂, increase availability of nutrients that plants need

prokaryotes are involved in the carbon cycle and nitrogen cycle

Prokaryotes and the carbon cycle

primary producers (plants and photosynthetic bacteria) use CO₂ in photosynthesis

consumers (animals and other heterotrophs) get energy from organic compounds made by primary producers and release CO₂ in atmosphere

decomposers (bacteria and fungi) breakdown dead plants and animals

Prokaryotes and nitrogen cycle

N₂ makes up 78% of atmosphere but is not usable by primary producers until bacteria do 3 things:

nitrogen fixation to convert N₂ into NH₄⁺ (N₂ is caught by bacteria in soil)

nitrification to convert NH₄⁺ into NO₂^- and NO₃^-, NO₃^- is then incorporated into plant tissue

ammonification to release NH₄⁺ during decomposition

• nitrates less harmful than ammonium

Photosynthesis: cyanobacteria

photosynthetic and aquatic - called '“blue-green algae”

only prokaryote that produces O₂

thought to have contributed to turning O₂ poor atmosphere into O₂ rich

• dramatically changed composition of Earth’s life since it ensured O₂ in atmosphere on early Earth

produce ‘blooms’ which can release toxins and reduce O₂

Symbiotic Relationships

Mutualism: ecological interaction that benefits both host and symbiont

• ex: bioluminescence, bacteria in our intestines

Commensalism: relationship that benefits one, while other is not harmed or helped

• ex: bacteria on our skin and in our GIT outnumber our cells by 1:10

Parasitism: parasite eats cell contents, tissues, or body fluids of host

• harm but do not kill host

• ex: Wolbachia spp.: bacterium that is the most successful parasite on the planet and targets the worlds most diverse group of animals (insects)

  • transmitted only by female hosts via eggs

  • bacteria benefits from skewed sex ratio with more females so it helps females reproduce without males, turns male embryos into females or kills off males before they even hatch

    • males eventually become resistant

Pathogens

bacteria cause about half of all human diseases

• ex: tuberculosis and lyme disease

produce poisons

• Exotoxins = proteins secreted by bacteria

• Endotoxins = lipopolysaccharide components of the outer membrane of gram-negative bacteria

pathogenic because it produces toxins or when the building blocks are toxic

Bacteria impacting plants

Pseudomonas syringae plant pathogen responsible for frost damage to crops

forms ice at temperatures above freezing - proteins in cell membranes change position of nearby water molecules so they fit more neatly into a lattice, antifreeze proteins help protect bacteria

used to generate artificial snow

Other applications of prokaryotes

CRISPR-Cas9 - helps defend against viruses by altering genes in any organism

Reduce reliance on petroleum by bacteria producing natural plastic, extracting and using to make durable biodegradable plastics, and scientists engineering bacteria to produce ethanol from agricultural waste and switchgrass and corn

Used in bioremediation to remove pollutants from soil, air and water

Central Questions/Key Points of bacteria and archaea

differences and similarities between 3 domains of life

explain bacterial reproduction and genetic recombination

what are cyanobacteria? why are they important for the plant?

explain how bacteria create ice

explain the 3 types of symbiotic relationships and provide an example of each

Eukaryotes

consist of animals, fungi, protists and plants

all eukaryotes have mitochondria

some have chloroplasts

eukaryotes more closely related to archaea

eukaryotes = nucleus (DNA enclosed in a membrane), prokaryotes = no nucleus

membrane-bound organelles

cytoskeleton: structural support, allows eukaryotic cells to have asymmetric forms and change shape and move and grow

most eukaryotes are protists

• most (but not all) protists are unicellular

most are multicellular

cells are much bigger in size

kingdoms: protists, fungi, plants and animals

Evolution to eukaryotes

don’t have a good idea of what evolved first

protist diversity

unicellular, colonial and multicellular

lots of ways of feeding: photoautotrophs, heterotrophs, and mixotrophs

asexual and sexual reproduction

Eukaryotic cell structures

autogenic origin: the modification of the plasma membrane into cellular structures (cell grows and membrane starts folding on itself and eventually makes complete separate compartment aka nucleus)

endoplasmic reticulum

golgi apparatus

nucleus

Endosymbiosis

how mitochondria and chloroplasts were acquired

prokaryote eats another prokaryote and it lives inside the other instead of being digested (archaea eats bacteria)

when one organism lives inside another and it typically benefits both organisms

Evidence of autogenic and endosymbiotic theory

mitochondria, chloroplasts, and bacteria = similar size

reproduce via binary fission

have single circular DNA

ribosomes are more closely related than ribosomes of eukaryotes

have really closely related DNA

both cellular structures have evolved once (no evidence that mitochondria and chloroplasts were acquired more than once)

archaea very similar to nucleus (archaean ate a bacteria, bacteria became mitochondria)

Algae ecologic role

produce about 50% of O₂

live in freshwater and seawater

phytoplankton makeup base of food webs (lots of things can eat them)

red, brown, and green algae

mostly unicellular, some multicellular (like kelp)

reproduce asexually, sexually and alternation of generations

like lego blocks, don’t have leaves or roots just mimics it

Photosynthetic protists

aquatic communities

• world’s photosynthesis:

  • 30% by protists such as diatoms, dinoflagellates, algae

  • 20% by photosynthetic prokaryotes

  • 50% by plants

human impacts

• additions of fertilizer can lead to blooms

• growth has declined in many ocean regions as sea surface temperatures increase

• warm waters can prevent upwelling of cold, nutrient rich waters that feed protists

Ciliates ecological role

allow cows to eat grass

animal-like protists

have cilia (little hairs) to move

have 2 nuclei (tiny micronuclei and large macronuclei)

live in water (almost everywhere)

eat bacteria and algae

reproduce mostly asexually (binary fission like prokaryotes)

can create feeding current to trap floating things

Symbiotic protists

dinoflagellates and coral polyps that build coral reefs

wood-digesting protists in the guts of termites

parasites: ex phytophthora ramorum caused sudden oak death and phytophthora infestans potato late blight (caused irish famine)

parasites: ex. malaria (caused by protist must have mosquito host and warm-blooded mammal (humans))

• undergo mitosis in liver then infects red-blood cells

• reduced ability to carry O₂

• meiosis in mosquito

Plasmodial slime molds ecological role

fungi-like protists

slime molds: no chitin in cell walls (diff. from mushrooms)

plasmodial slime molds: start as single-cells → combine to have many nuclei, hunt for food (detects chemical, grows towards it), decomposers

Reproductive terminology

haploid = single set of unpaired chromosomes (n)

diploid = 2 sets of chromosomes (2n)

gamete = male or female germ cell (n)

zygote = product of joining of gametes (fertilized egg, 2n)

gametophyte = multicellular haploid stage produces gametes

sporophyte = multicellular diploid stage produces spores

Alternation of generations

not in animals

plants and some algae: haploid multicellular organism (gametophyte) → diploid multicellular organism (sporophyte), meiosis produces spores that then germinates, algae spores go into water and can grow plant-like structure that then produces gametes

most fungi and some protists: haploid unicellular or multicellular organism → zygote

every second generation looks like itself

Central Questions/Key Points Protists

what are the defining features of eukaryotic cells?

endosymbiosis contributed to protist diversity — mitochondria and plastids were prokaryotes engulfed by early eukaryotic cells

describe the alteration of generations for multicellular algae

describe the malaria life cycle

go over the reproductive terminology slide — useful forever in biology

explain the importance of photosynthetic, symbiotic and parasitic protists

Why we care about plants

produce O₂

provide food

consume CO₂

economically important (ex: food, health, raw materials, furniture)

Main concepts: plants transitioning to land, what early land plants on Earth were like, and plants gaining biomass

Protists and plants

plants are closely and well related to algae

the adaptations green algae (charophytes and protist) needed to develop to move to land including factors of needing light, CO₂ and O₂

Limiting factors for plants living on land

gravity (in water they had buoyancy)

light energy (stronger)

gas exchange (CO₂ and O₂), more O₂ on land and too much oxygen gives you genetic damage (cancer)

water

nutrients (isn’t just floating around in water anymore)

How plants dealt with gravity

algae had to grow structures that contained air bubbles to help them float

on land:

• land plants have tough structures to support their weight (wood, stems)

  • roots anchor them into the ground

  • stem is necessary

  • roots pick up nutrients and water

• roots stabilize plants on land

• evolved ways of moving water and nutrients against the force of gravity (xylem and phloem)

How plants dealt with light energy

underwater light dissipates quickly (not enough light for photosynthesis)

on land:

• too much light, sunlight damage

  • UV light damage

• evolved systems to prevent light damage

Green algae ancestor (charophyte)

plant and fungi relationship

• communicate and exchange nutrients (need roots for nutrients)

• give nutrients to fungi and fungi gives to plant (symbiotic relationship)

plants and algae both: eukaryotes, photosynthetic autotrophs, cell walls made of cellulose, and chloroplasts

Major plant groups

1. non-vascular plants: small, not good at transporting water

2. vascular plants without seeds: can transport water over longer distances

3. vascular plants with naked seeds

4. vascular plants with protected seeds

Non-vascular plants (byrophytes)

mosses, liverworts, hornworts

low growing with sprawling growth

small plants

prefer moist environments (can’t reproduce if too dry)

lack vascular tissue which is why they remain low to the ground

lack leaves, seeds, flowers and roots

use rhizoids to anchor to the ground (fake roots, acts like velcro)

gametophyte (n) is the dominant life stage (leafy part)

unicellular spores

sporophyte grows on trop (rusty color)

Life cycle: alternation of generations

• sperm of moss needs water to get to the egg (water is needed to reproduce)

  • reproductively active moss = diploid sporophyte and haploid gametophyte

  • “kids that never move out”

Vascular plants

lycophytes and monilophytes

ferns, club mosses

vascular tissue

true leaves, stems and roots

lignin to strengthen cell walls

grow taller

sporophyte (2n) is the dominant life stage

• reproductive structures of ferns called sori are present on leaves and release spores

  • can cross fertilize or self fertilize

  • sporophylls = modified leaves that bear sporangia (clusters = sri)

    • lycophytes and gymnosperms produce strobili and angiosperms produce carpels and stamens

  • most seedless vascular plants are homosporous (1 type of sporophyll that produces one type of spore → develop bisexual gametophyte)

structure of vascular plants:

• leaves (primary photosynthesis organ)

• stem (structural support)

• roots (absorb water and nutrients, store food)

• xylem (water and nutrient transport) = vascular tissue type

• phloem (sugar, amino acid transport) = vascular tissue type

Evolution of Seed Plants

1. Seeds (land adaptation)

• embryo and food supply, surrounded by a protective coat (protection and nutrition)

• multicellular which is better for land (no longer single-celled spores)

• can remain dormant for a long time up to years just need to wait for water to be added

• can be carried long distances away from parent plant (dispersal)

2. Reduced gametophytes

• most gametophytes are microscopic

• develop from spores retained within the sporangia of sporophyte (provides protection and nutrition)

3. Heterospory

• produce male and female gametophytes (megasporophylls - megaspores → female, microsporophylls - microspores → male)

4. Ovules

• female gametophyte is protected

• megasporangium is retained within the parent sporophyte

• protected by integument = layer of sporophyte tissue

• together called an ovule and the female gametophyte develops from the megaspore that produces one or more eggs

5. Pollen (land adaptation)

• male gametophyte within a pollen wall = pollen grain

• can be carried by wind or animals — no water needed (can do everywhere)

• sperm does not need motility — carried to egg by pollen tube (no longer has to swim to it anymore)

Ex: sequoias (coniferous trees)

Traits of vascular plants with naked seeds (gymnosperms)

Ex: conifers, cycads, ephedra

seeds not enclosed in ovary (“naked seeds”)

produce seeds and cones

do not produce flowers or fruits

most are tall and woody

typically found in colder regions

sporophyte (2n) is the dominant life stage

sporangia located on strobili or cones = modified

most evergreen, some deciduous

4 phyla: ginkgophyta = only Ginkgo biloba lives today, flagellated sperm, dichotomous venation; Cycadophyta = palm-like, flagellated sperms, 75% of species are threatened; Gnetophyta = common species are Ephedra, produces alkaloid ephedrine, decongestant, heart stimulant, used in weight loss supplements; Coniferophyta = pine, spruce, fir, cedar, juniper, cypress, sequoia, most evergreen with needle-like leaves, excrete resin that can seal wounds and deter pests, monoecious: ovulate cones and pollen cones on the same individual

Life cycle of Gymnosperm Coniferophyta

2 cones produces (reproductive structures), male gametophyte = 1 cell, female cones need to meet with male gametophyte to then get zygote, they prevent self fertilization by avoiding both gametophytes at the same time

Vascular plants with protected seeds (angiosperms)

they have a sepal, petal, stamen, and carpel

flower helps with reproduction

stamen = male reproductive (produce pollen)

carpel = female reproductive (hidden on the inside of a flower)

job is to attract pollinators

prevent self fertilization by developing stamen and carpel asynchronously

zygote incorporated into fruit

only 1 ovule needs to be fertilized for fruit to develop (not all of them)

flowering plants with single phylum = Anthophyta

Monocots and Dicots

monocots = 1 cotyledon, parallel leaf venation, scattered stem vascular tissue arrangement, fibrous root system with no main root, 1 pollen grain opening, multiples of 3 for number of flower petals/organs

dicots = 2 cotyledon (recent DNA studies have shown this group is paraphyletic and a vast majority is now known as Eudicots), net or web leaf venation, ring or circle stems vascular tissue arrangement, taproot aka main root usually present root system, 3 pollen grain openings, multiples of 4 or 5 for number of flower petals/organs

cotyledon = the structure that will become the first leaf and root which matters because it influences growth (how it gets nutrients with branched or non-branched root system, do you get a tree or a bush, etc.)

Derived Traits of plants

alternation of generations - evolved in some algae (both haploid and diploid stages are multicellular)

multicellular, dependent embryos - plant embryos develop from zygotes, retained within female parent: get protection and nutrients

walled spores produced in sporangia - plant spores = more complex and protected, haploid reproductive cells, grow into multicellular haploid gametophytes by mitosis, sporangia = produce the spores: diploid sporocytes undergo meiosis to produce haploid spores

multicellular gametangia - gametes produced in multicellular organs called gametangia, independent life stage, female gametangia = archegonia, male gametangia = antheridia, egg fertilized within the archegonium and develops into embryo

apical meristems - what allows plants to grow vertically (plants can grow forever), regions at growing tips of plants where cells divide repeatedly

Plants gaining biomass

photosynthesis at the center

also need nutrients other than glucose

Plants and gas exchange

especially important for parts involved in photosynthesis

bottom side of every leaf has openings (stomata)

Central Questions and Key Points

the derived traits of plants: alternation of generations, multicellular/dependent embryos, walled spores produced in sporangia, multicellular gametangia, apical meristems

plant groups are further divided by the presence of vascular tissue, presence of naked seeds or presence of protected seeds

the significance of seedless vascular plants int he Carboniferous period

nonvascular plants have haploid gametophytes as the dominant life stage whereas seedless vascular plants and naked seed plants and protected seed plants have diploid sporophyte as dominant life stage

describe the life cycle of nonvascular plants (moss), seedless vascular plants (fern), naked seed plants (pine) and protected seed plants (angiosperms)

describe the following adaptations for life on land for seed plants: seeds, reduce gametophytes, heterospory, ovules, pollen

gymnosperms are a major group of naked seed vascular plants - describe the Ginkgophyta, Cycadophyta, Gnetophyta, and Coniferophyta groups

angiosperms are a major group of protected seed vascular plants, also called flowering plants - describe the monocot and dicot groups

Carboniferous period

350-300 million years ago

large drop in CO₂:

• global cooling which resulted in widespread glacier formation

• roots secreted acids that broke down rocck

• released calcium and magnesium reacted with dissolved CO₂

• washed into ocean and formed calcium and magnesium carbonates

plants became coal:

• trees died and did not completely decay

• turned into thick layers of peat

• covered by sea and marine sediments

• years of heat and pressure = coal