bio94 midterm 2 review

tree of life consists of what

bacteria, archaea, eukarya

common ancestor in tree of life had what characteristics

characteristics common to life — dna use, same 20 amino acids (tree thinking)

monophyletic group

group that contains all the descendants from a common ancestor

which branches of the tree of life are considered a monophyletic group?

all domains of life : bacteria, archaea, eukarya

are prokaryotes a monophyletic group? which domains of life do they consist of?

no prokaryotes are not a monophyletic group, they consist of bacteria and archaea (paraphyletic : not all descendants of an ancestor)

can prokaryotes be multicellular? are the vast majority of prokaryotes single celled or multicellular?

yes (some are simple multicellular organisms) but a majority are single celled

simple definition of multicellular organisms

multiple cells, some of which are differentiated

give an example of a multicellular prokaryote?

cyanobacteria

are eukaryotes or prokaryotes the most abundant organisms on earth?

prokaryotes

in a human body, are there more eukaryotic or prokaryotic cells — where do they reside

more prokaryotic cells — reside in our mouths, tracts, skin, etc

what are prokaryotes important for? name a few examples

biological function — ecology of soil, growth of plants, life underwater, human medicine and functioning of ecosystems

examples of diseases from prokaryotes

strep throat, diarrhea, black plague, gonorrhea

why is bacteria important for human health? what can imbalances cause?

balance of the right bacteria is critical to thrive, and imbalances cause the harmless bacteria to grow out of control

clostridium difficile — occurs when, causes what

a type of bacteria in intestines, and when balance in gut changes and c.diff overgrows. it releases toxins attacking lining of intestines causing CLOSTRIDIUM DIFFICILE COLITIS

how is clostridium difficile colitis treated?

antibiotics usually, but can also transplant feces into someone who is sick (90% cure rates)

ways to study the diversity of prokaryotes

1) enrichment culture

2) dna sequencing (metagenomics)

3) shape recognition

4) gram stain

5) modes of nutrition

describe enrichment culture

culturing and grown in the lab by providing conditions to coax bacteria — ONLY SMALL PROPORTION OF PROKARYOTES CAN BE GROWN

describe dna sequencing of prokaryotes — also called what?

sequencing prokaryotic dna from an environmental sample (can be from humans too) and sequencing all dna/or ribsomal dna for a barcode of a species. this method can be used for seeing number of species and relative abundance of each one b/c each prokaryotic species has dna sequence reflecting phylogenetics — can be called METAGENOMICS.

describe shape diffs of prokaryotes

either spherical (coccus) or rod shaped (bacilli) or helical

bacillus

rod shaped

example of the helical shape in bacteria — causes what

treponema pallidium — causes syphilis b/c corkscrew/helical shape of bacteria screws its way into breaks of skin to multiply

describe gram stain

provides insights into composition of cell wall/plasma membrane by applying chemical treatments (including violet dye and iodine)

why is the gram stain significant

distinguishes diff bacteria and can be used to culture bacteria to aid identification and devise appropriate treatment

gram positive bacteria

retains violet dye (violet/purple)

gram negative bacteria

do not retain violet dye (pink)

differences between gram positive and gram negative

gram + have more peptidoglycan and gram- cells contain less

what is peptidoglycan

carbohydrate forming cell wall that absorbs violet dye of gram stain and causes cells to turn violet when being stained

which type of bacteria is penicillin more effective on?

gram positive b/c it prevents synthesis & cross linking of peptidoglycans — but in gram negative it’s harder to access peptidoglycans b/c its in the middle of the cell membrane aka less effective on -

gram positive examples of disease bacteria — shape, arrangement, and diseases caused

1) streptococcus pyogenes (spherical shape : chain — causes strep throat, scarlet fever, rheumatic fever)

2) streptococcus pneumoniae (spherical shape : chain — bacterial pneumonia)

3) staphylococcus aureus (spherical shape : bunch of grapes — skin infection, toxic shock)

gram negative examples of disease bacteria — diseases caused

1) salmonella enterica — food poisoning

2) neisseria gonorrheae — gonorrhea

why is gonorrhea significant?

2nd most common disease in US, 50% cases are 19-24 years old, more susceptibility for women and can be asymptomatic — growing antibiotic resistance

out of bacteria and archaea, which DO NOT contain peptidoglycan in cell walls

archaea

describe modes of nutrition of prokaryotes

1) autotrophs

2) heterotrophs

autotrophs — types

DO NOT need organic compounds for food — need CO2 and energy source to synthesize organic compounds

1) photoautotrophs

2) chemoautotrophs

photoautotrophs

use light as energy + co2, and synthesize organic compounds through photosynthesis

photosynthesis equation

photosynthesis facts

1) complex

2) glucose used as raw material to make other organic compounds needed (nucleotides, amino acids, etc)

3) byproduct = o2, photosynthesis changed atmospheric composition around 2.3 billion years ago

4) unknown evolution

5) life is dependent on photosynthesis for oxygen rich atmosphere and photosynthetic organisms = 1st to colonize land from oceans + are food source for non photosynthetic

chemoautotrophs — unique feature?

energy from chemical bonds + co2 — via oxidation of donors in environments

common chemicals = h2s, nh3, organic compounds. they can also support life in absence of light

equation for sulfur oxidizing bacteria

h2s into sulfate + energy

deep sea vent community — relation to chemoautotrophs

communities dependent on chemotrophic bacteria (and archaea) for energy, and most larger organisms that exist live in symbiosis with chemoautotrophic bacteria, most freeliving bacteria in deep sea vents are archaea (adapted to extreme environments)

symbiosis

relationship between organisms of diff species that live together in contact

deep sea symbioses

mutualistic — both parties benefit

ie. riftia tube worms helping bacteria concentrate on h2s and oxygen and receiving organic carbons (tube worm = host)

are deep sea symbionts bacteria or archaea

bacteria

thermophiles

archaebacteria adapted to high heat environments

heterotrophs

require source of organic carbon in food — cannot synthesize on their own

1) photoheterotrophs

2) chemoheterotrophs

photoheterotrophs

organisms capable of capturing energy from light via photosynthesis but also requiring organic compounds — CAN make glucose but not all compounds needed from a glucose precursor

chemoheterotrophs

consume organic compounds for energy/carbon source — most prokaryotes, humans, animals, and fungi

synapomorphy

trait present in ancestral species and shared exclusively by evolutionary descendants

what is a synapomorphy for bacteria

peptidoglycan in cell walls

archaea vs bacteria

archaea : no peptidoglycan in cell walls, no diseases in humans, one type of RNA polymerase (13 subunits — similar to rna polymerase II), methionine as 1st amino acid, histones associated with dna

bacteria : peptidoglycan + can cause disease, one type of RNA polymerase (5 subunits), formylmethionine as 1st amino acid, histones NOT associated with dna

BOTH : prokaryotes (usually unicellular), similar structures (flagella and circular dna), asexual reproduction aka BINARY FISSION, haploid

cyanobacteria

photoautotrophic + multicellular

protist

all eukaryotes that ARE NOT of plants, animals and fungi

are protists monophyletic

NO, paraphyletic (some but not all descendants from common ancestor

diffs between eukaryotes and prokaryotes

nucleus, mitosis, meiosis, mitochondria/chloroplast, linear chromosomes, diploid, complex (not simple) multicellularity

how did prokaryotic cell turn into eukaryotic cell?

1) origin of nucleus

2) endosymbiotic incorporation of prokaryotic cells into mitochondria/chloroplast

describe origin of nucleus

nuclear envelope likely formed through invagination, eukaryotes pack dna into chromosomes, undergo mitosis and also have a diploid phase of life cycle.

giardia lamblia

PRIMITIVE EUKARYOTE — protist showing link between prok and euka. it contains two HAPLOID nuclei : haploid proka —> primitive euka w/ 1 haploid nucleus —> primitive euka w/ 2 haploid nuclei —> euka wih single diploid nucleus.

also has dna in chromosomes packed with histones, and mitochondria (likely formed early in branch leading to euka)

describe endosymbiotic incorporation of prokaryotic cells to form mitochondria and chloroplasts — engulfed what, how many events of origin for each, and function of each one

1) mitochondria occurring via endosymbiosis of AEROBIC HETEROTROPHIC prokaryote (responsible for cellular respiration and breaking down pyruvate to release co2, h2o and energy to synthesize compounds) — IN ALL EUKARYOTES (just one event of evolution)

2) chloroplasts : euka engulfing PHOTOSYNTHETIC CYNOBACTERIUM — found in plants generally not in animals/fungi — originating in multiple endosymbiotic events (1st of which led to evolutionary branch of plants)

endosymbiotic theory

1) prokaryote engulfed by phagocytosis by primitive euka

2) proka not digested but acted as endosymbiont helping cellular metabolism

3) host and endosymbiont lost ability to exist on own b/c of mutualism

evidence for endosymbiotic theory

1) chloroplast + mitochondria right size to come from proka

2) membranes have enzyme/transport systems of prokas

3) organelles have splitting process similar to prokas (fission not mitosis)

4) have circular dna like prokas

5) machinery for dna rep and trans aka once free living

6) molecular systematics show genes as proka like, less similar to euka genes

primary endosymbiotic event for chloroplasts led to what

leads to plants

secondary endosymbiotic event

primitive eukas with a chloroplast engulfed by ancestral protist — euka with chloroplast engulfed by another euka

foraminifera — type/description/used for what

protist/single celled/heterotrophic with caco3 shells — 4k species in oceans, 40 of which are planktonic (floating in water) and rest live on the bottom

they have an extensive fossil record and are used to estimate climate changes (b/c of abundance, wide distribution and sensitivity to environmental variations)

trichonyma — type/function

euglenid protist — lives in termite guts to help digest wood

plasmodium falciparum — type + causes what

apicomplexans parasitic protozoa : causes malaria

plasmodium life cycle

two hosts : human and mosquitoes (parasitism)

mosquitoes : bite while having plasmodium —> into blood

human : proliferates in liver —> differentiates in red blood cells and features male and female parasites : most of life cycle = haploid with male/female gametes —> mosquito bites and gametes make zygote —> produces mosquito baby infected by plasmodium

dinoflagellates — classification/species #/nutrition mode/shell type

unicellular algae with ½ being autotrophs (some parasites) — 4k species and covered by hard shells of cellulose and silicate with flagella to propel them through — most = plankton (free drifting)

why are dinoflagellates important?

serve as food source for fish or marine/freshwater animals — can encounter conditions to proliferate and cause a RED TIDE (usually harmless but can release toxic substance to cause death to other species)

algae — function/types

plant like protists, mostly : autotrophic, aquatic, and multicellular, fixes carbon through photosynthesis

1) red, green, brown

is algae monophyletic?

no, paraphyletic (not all descendants of a common ancestor)

what algae is closest related to land plants?

green

brown algae

multicellular, photosynthetic kelp and goes through alternation of generations (some time in diploid and haploid in life cycle) — helped make gunpowder in wwii, to eat, additives, etc

green algae

multicellular, photosynthetic, ancestor to land plants, alternation of generations

diversity amongst protists

1) multicellularity

2) chlorophyll (euka autotrophic algae have chlorophyll a)

3) go through sex (haploid gametes of separate sexes to make diploid zygote)

4) algae = ancestor of land plants

5) alternation of generations (multicellular diploid and multicellular haploid phases)

chlorophyll in algae

green : a,b

red : a

brown : a, c

algae life cycle — type, what is dominant, are gametophytes independent?, are sperm motile?

PROTIST

dominant diploid sporophyte (2n) creates haploid spores through meiosis

— haploid spores can be male or female

haploid spores make haploid gametophytes (male and female) through mitosis

haploid gametophytes make gametes through mitosis in structures (also male and female)

haploid gametes (sperm and egg) come together to fuse(syngamy) to make a diploid zygote

diploid zygotes go through mitosis to make sporophytes — repeat!

highlighted things about algae alternation of generations — features of spores/sperm in aquatic

1) gametophyte and sporophyte look identical despite being haploid diploid respectively

2) spores and sperm have flagella b/c they need to swim (aquatic environment) — reproduction requires water

plants

first multicellular photosynthetic autorophic eukaryotes to survive and reproduce on land

required innovations for move to land

1) sexual reproduction on land — leading to embryrophyte formation

—> all land plants = embryophytes with alternation of generations

2) ability to survive on land/in contact with air : no homogenous environment with contact with nutrients and medium of support

—> formation of cuticle, stomata and vascular tissue

embryophytes

organisms with a structure that nourishes and protects developing diploid embryo

cuticle — common to what

waxy layer helping plant retain moisture in tissues — all plants

stomata

pores for gas exchange of co2 and o2, found on leaves — all plants

vascular tissue — purpose and response to what?

response to heterogeneous environment — transporting water/nutrients through body, supporting upright structure, and preventing desiccation (drying out)

evolutionary sequence of land plants — rankings of species + innovations

1) nonvascular plants (origin of embryophyte) 3rd largest # of species

2) seedless vascular plants (vascular tissue — some nonvascular contain rudimentary vascular tissue but not homologous to the vascular tissue in these palnts) 2nd largest # of species

3) gymnosperms (seed plants : naked seeds) least # of species

4) angiosperms (flowering plants) largest # of species

common non vascular plants — first and second name are what, limited by what

moss, hornworts, liverworts — embryophytes with waxy cuticle and stomata, a difficult time getting nutrients/water from soil to leaves and are limited to moist environments + short stature

CAN ALSO BE CALLED BRYOPHYTES

moss life cycle — type, what is dominant, are gametophytes independent?, are sperm motile, how are seeds dispersed?

NONVASCULAR PLANT

dominant haploid gametophyte with mature diploid sporophyte on top, going through meiosis to produce separate male and female haploid spores.

spores dispersed by wind (less reliance on water)

spores go through mitosis to go make haploid male and female gametophytes (independent of e/o)

haploid gametophytes make haploid gametes through mitosis —> sperm developing in ANTHERIDIA, egg in ARCHEGONIA

sperm swims to egg for fertilization (reliance on water b/c moss is near rivers) to make diploid zygote in archegonium (prevents dessication to protect eventual embryo)

diploid zygote in archegonium going through mitosis to make embryo then again into developing diploid sporophyte, which grows out of the top of the haploid gametophyte

roots

subterranean to anchor plant and absorb water/minerals

leaves

aerial portions of the plant, site of photosynthesis

shoots

function to support the plant and important to transport system

seedless vascular plants — description

embryophytes, development of vascular tissue to get water transported easily across plant, continued sperm swimming/reliance on water to reproduce, independent looking gametophyte

vascular tissue

moves water, nutrients, food up and down plant AND supports plant so they can grow larger

xylem — direction, and types

vascular tissue that transports water from roots to leaves, to shoots, and minerals/nutrients from soil/roots to other parts of the plant

also provides support so plants can grow larger than a few ft on land (in water, support already provided)

— GOES UPWARD

1) tracheid

2) vessels

tracheid — direction and type of tissue, cells contain what

xylem vascular tissue that is thin with tapered ends and perforated cells(pits) at ends/sides, cells laid end to end, DEAD TISSUE, empty — basically a straw like tube where water goes from roots to leaves (UP!). cells contain lignin

xylem sap

water and nutrients moving w/o hindrance of cellular cytoplasm (b/c of dead tissue)

lignin — what wall and which xylem type

hard material providing support for plant’s secondary wall, forming long hollow tubes (VESSELS AND TRACHEIDS)

what is the primary wall of a tracheid formed from? what type of xylem

cellulose — both

transpiration-cohesion process

process of xylem sap moving up xylem — largely facilitates growth of vascular plants hence why nonvascular is small

1) transpiration aka evaporated of water from leaves into air through stomata — moving towards cells that have low water b/c water moves towards areas of low conc

2) water is cohesive, meaning whole columns of water move in response to evaporation from leaves

3) water sucked out top of straw via from leaves via evaporation

4) no energy needed

5) water transported up shoots into leaves at 15 m per hour or faster — speed fueled by transpiration

6) 90%+ water transported via xylem sap lost by evaporation

7) water column is also a support mechanism for the plant

vessels — description

wider shorter straws with ends more open, serve to transport water more efficiently, perforated and pits at top

have vessels evolved just once or more than once?

originated more than once and in ancestor of angiosperms — explains why angiosperms more efficient than other plant groups

phloem

vascular tissue taking compounds like glucose towards roots b/c they cannot do photosynthesis — GOES DOWNWARD (leaves to roots)