Unit 1 D+E

Chap. 1, 26, 27, 28

The scientific method order

• ask a question

• do background research

• construct a hypothesis

• (educated guess) if, then statement

• test w/ experiment

• analyze results/draw conclusions

• hypothesis is true/false (a conclusion of no effect is still a conclusion)

• report results

discovery sceince

observational/descriptive (natural history)

hypothesis science

hypothesis = tentative answer to a well framed question — leads to predictions that can be tested by EXPERIMENTATION

a hypothesis must be…

testable and falsifiable (able to be proven false)

• failure to prove a hypothesis does not prove it

theory

broader than a hypothesis, it can lead to testable hypothesis , has to be supported by a lrg. body of evidence and has been validated by lots of experiments (over many diff. spaces and times)

ex.) inheritance, nat. selection, cell theory, homeostasis, and evolution

limitations of science

observations/experiments must be repeatable

• science cannot support/falsify supernatural explanations which are out of the bounds of science

evolution accounts for…

the unity and diversity of life—it is the process of change that has transformed life on earth, natural selection is the mechanism

what does almost every organism have

a mother and a father

charles darwin

origin of species (1859)

made 2 points:

• species showed evidence of descent w/ mods. from common ancestors

• natural selection is the mechanism behind descent w/ mod.

darwins observations

• individuals in a population have traits that vary

• many of these traits are heritable (passed parents —> offspring)

• more offspring are produced than survive

• competition is inevitable

• species generally suit their environment

speciation// individuals best suited to their environment =

more likely to survive and reproduce (fitness)

organism has accumulated enough differences they can no longer mate and reproduce

2 things behind genetic variation

gene recombination and mutation (change in genetic code)

taxonomic groups from broad to narrow

• domain

• kingdom

• phylum

• class

• order

• family

• genus

• species

dear king phillip come over for good soup

** each individual unit is called a TAXON

genus + species =

bionomial nomenclature

2 categories —> 5 categories —> 3 categories (or domains)

2 - plant or animal?

5 - monera (prokaryotes), protista (unicellular eukaryotes), plantae, fungi, animallia

3 [current] - domain bacteria, archaea, domain eukarya

known species versus acc. # of species on earth

1.8 mil. have been named to date (thousands more identified yearly)

• 10-100 mil. = estimated total # of species that acc. exist (the brunt of that # is bacteria, organisms, ocean, insects)

what unifies all life?

DNA is the universal genetic lang. common to all organisms

systematics

‘systema’ meaning organized whole

discipline of classifying org. to determine their relationships

taxonomy

‘taxis’ meaning order arrangement

ordered division and naming of organisms

phylogeny/phylogenetic classification/trees

‘phylon’ meaning clan, tribe, or race

the evolutionary history of a species or group of related species (phylogenetic trees)

phylogenetic classification shows us patterns of descent - allows us to identify similar genes in organisms —> more similarities = closer relationship

phylogenetic tree = evolutionary tree (history) what evolved from what, in what order, and when

• looking at sequence similarities between DNA

common genetic sequences = common ancestry

cladistics

‘klados’ meaning branch

sub-discipline of systematics that groups by common descent (connecting organisms)

classification

needed to organize diverse species in a way that makes sense (think organization in a library or grocery store)

bionomial nomenclature

2 part names for species

bi = 2

nomen = name

• Carolus Linnaeus, Swedish biologist

• hierarchal classification

• universal term used by scientists

how to write correctly - genus + specific epithet (species)

• capitalize only the Genus (first part)

• keep the species (second part) lowercase and italicize both

ex. Homo sapiens

biological hierarchy (11)

ordered set of items arranged in levels (usually of complexity)

• biosphere

• ecosystems

• communities

• population

• organism

• organs and organ systems

• tissues

• cells

• organelles

• atoms

• molecules

biosphere

earth // all areas on earth where life exists

ecosystem

all living (biotic) and non-living (abiotic) things in an area within environment (atmosphere too)

community

all populations inhabiting a particular area

population

all individuals of a species in a specific area

organism

an individual living entity

organs/organ systems

different tissues functioning together / organs interacting to perform complex functions

tissue

a group of similar cells working together

cell

the basic unit of structure and function in living things

organelle

functional components within cells e.g. mitochondria

molecule

two or more atoms bonded together

atom

the fundamental unit of matter

3 domains of life

bacteria, archaea, and eukarya

the characteristics of eukarya (of the 3 domains of life)

includes single or multicellular organisms with complex, membrane-bound organelles

(plants, animals, fungi)

the characteristics of bacteria (of the 3 domains of life)

single celled organisms with peptidoglycan cell walls (what gets stained)

bacteria are prokaryotes

the characteristics of archea (of the 3 domains of life)

archaea are single celled, often extremophiles with unique cell membranes lacking peptidoglycan

archaea are prokaryotes

the difference between prokaryotes and eukaryotes

the presence of a nucleus and membrane-bound organelles

eukaryotes - larger, complex cells with DNA enclosed in a nucleus

prokaryotes - smaller, simpler, unicellular organisms with free floating DNA (in nucleoid region)

prokaryote structure

nucleoid (DNA area), ribosomes, plasma membrane, cell wall, capsule, pili, flagella

eukaryote structure

nucleus, endoplasmic reticulum, golgi apparatus, mitochondria, lysosomes, cytoskeleton

what do hatch marks/branch points mean in a phylogenetic tree

branch points (nodes) in a phylogenetic tree represent the most recent common ancestor of two or more lineages that have diverged, signaling a speciation or divergence event

hash marks/tick marks indicate the evolution of specific, derived traits or character changes along a lineage

homology

similarity due to shared ancestry (sharing similar characteristics with your family tree) - derived from a common ancestor

analogy

is similarity (comparable) due to convergent evolution

convergent evolution

similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary linkages

ORGANISMS COME TOGETHER (BECOME SIMILAR) BECAUSE OF THE WAY THEY EVOLVED

divergent evolution

accumulation of differences between closely related populations within a species that an lead to speciation (they are now 2 separate species/genomes = no longer compatible)

speciation

the evolutionary process by which populations evolve to become distinct, reproductively isolated species

sorting homology vs. analogy

this comes from fossil evidence and the degree of complexity (more complex = more likely to be homologous bc/ the probability of highly specific structure evolving twice is extremely low)

clades

grouping of organisms (incl. single common ancestor and all of its based on shared derived characteristics and common descent, both living and extinct)

ingroup

group studied

outgroup

group not part of ingroup

clades are organized/described in 3 ways

monophyletic, paraphyletic, and polyphyletic

monophyletic

consists of the ancestor species and all its descendants

paraphyletic

group consists of common ancestor but not all descendants

polyphyletic

group includes many species that lack a common ancestor but share similar characteristics

the best hypothesis for phylogenetic trees

fit the most data: morphological, molecular, and fossil

morphological homology

integrated features (structural) of an organism —> similar body structures due to shared ancestry (this increases the more closely related organisms are in taxonomic hierarchy)

prokaryotes (what they are and what they do)

thrive almost everywhere, incl. places too acidic, salty, cold, or hot for most organisms

• ubiquitous = meaning they are everywhere/very common (billions)

• single celled

• microscopic

• small

• tiny but mighty

prokaryotes (bacteria/archea) play a maj. role in the recycling of chemical elements functioning as decomposers (break down corpses/dead things) some prokaryotes add usable nitrogen into the environment - play a huge role in our bodies (nitrogen fixers)

2 domains of prokaryotes (bacteria and archaea) - domain archaea

kingdom archebacteria

• cell walls = polysaccharides and proteins, cell membranes

• ribosomal RNA differ significantly from bacteria

contain polysaccharides and proteins but lack peptidoglycan

extemophiles

live where nothing else can

extremozymes

enzymes that can handle really extreme conditions and temps (even anaerobic conditions)

extreme thermophiles

heat

max. catalytic activity at 75-80 degrees celsius

taqs polymerase can replicate DNA @ really high temps.

PCR allows rapid amplification (making billions of copies) of small sample of DNA using high temperature process (Kary Mullis invented PCR)

extreme halopiles

lots of salt

methanogens

no O2 (anaerobic), use CO2 to oxidize hydrogen

acidophiles

acid

alkophiles

basic

2 domains of prokaryotes (bacteria and archaea) - domain bacteria

where bacteria is located in our bodies

• scalp - dandruff

• armpits

• poop

• feet

• mouth

• all over our skin

• hair follicles

• vagina

• gut

microbiota

set of microscopic organisms (that live on and in human body)

• microbiome = all of the orgs. that coexist in our bodies

symbiosis

ecological relationship in which 2 species live in close contact - larger host, smaller symbiont

close long term interaction between different species living together

• can be mutualistic, parasitic, or commensalist

mutualism

both benefit

commensalism

1 org. benefits while neither helping/harming other (much)

parasitism

1 org. gets benefits but harms host (harms but not kills)

• parasites that cause disease = pathogens

bacteria are classified and identified by…

shape (often in the name) and staining properties (gram + or gram -)

3 most common shapes

spheres (cocci), rods (bacilli), and spirals

arrangement of cocci

spherical shape/arrangement

cocus

diplococci

tetrad

sarcina

staphylococci

streptococci

arrangement of bacilli

rod

baccillus

diplobacilli

streptobacili

palisade

coccobacilli

arangements of spiral

spirochetes (spagetti)

spirilla (helical shape, corkscrew form)

vibro (Cheetos)

gram stain

classifies many bacterial species into gram negative or gram positive based on cell wall composition

gram neg. bacteria

have less peptidoglycan (what stains) and an outer membrane that can be toxic, and they are more likely to be antibiotic resistant

• stain red

outer membrane —> peptidoglycan layer —> plasma membrane

outer membrane = protective barrier to phagocytosis, antibiotics, detergents, lysosomes, heavy metals

gram positive bacteria

thick peptidoglycan layer

positive purple peptidoglycan

• strain purple

cell wall (peptidoglycan layer) —> plasma membrane

every bacterial cell has

cytoplasm (cell soup), ribosomes (proteins), plasma membrane, nucleoid (cont. DNA, circular chromsome NOT enclosed by membrane)

most bacteria have but not all

cell wall, plasmid, pilus, capsule, fimbriae, flagella

bacterial cell well

maintains cell shape, provides physical protection, prevents cell from bursting, contains peptidoglycan, network of sugar polymers cross-linked by polypeptide

endospores

seed-like

when conditions are poor, endospores formed for survival

• withstand harsh conditions

• resistant to high temps and desiccation (drying out)

• can last for centuries

flagella

structures used by motive bacteria for propulsion; many species can move toward or away from certain stimuli —> most motile bacteria propel themselves by flagella, many bacteria exhibit

• chemotaxis - chemicals

• phototaxis - sun/photosynthesis

bacterial and eukaryotic flagella are analogous structures evolved independently to serve a similar purpose (movement) not descending from a common ancestor

fimbriae

‘pili’ short hair like appendages, crucial for adhesion, helping bacteria stick to host tissues, surfaces, or each other to form biofilms

capsule

protection and adhesion

• virulence factor (enables bacteria to invade hosts immune system)

• prevents phagocytosis = outer layer acts as a phagocytic shield, preventing immune cells from fighting off bacteria

pilus

straw-like appendage that facilitates conjugation (horizontal transfer of genetic material)

plasmid(s)

small circular DNA molecule separate from main chromosome, replicated independently and often carries beneficial genes like antibiotic resistance (can share this with other bacteria, crucial for adaptation)

• R plasmids = carry genes for antibiotic resistance (antibiotics kill sensitive bacteria, not those with R plasmids)

• F Plasmids = genes for fertility, have to have the ability to pass on resistance (transfer of genetic material) happens through the pilli

cell wall

(rigid non-living protective outer layer found only in plants, fungi, and bacteria, providing structural support, fully permeable)

bacterial reproduction

binary fission (asexual reproduction/cell division) single parent cell replicates its DNA and splits into two identical daughter cells of equal size

• reproduce every 1-3 hours

• logarithmic growth (starts fast, slows over time)

• mutations accumulate rapidly (sheer numbers = lots of mutations)

genetic recombination

no sexual reproduction, bacteria just divide

• makes copies of itself

• in eukaryotes, meiosis is where G.R. happens

• bacteria are always changing and evolving bc/ of mutation (change by copying error)

• transduction-new sequence introduced (transduction or conjugation)

transduction-new sequence

from bacteriophage (type of virus that replicates inside bacteria/infects bacteria cells)

piece of DNA/RNA that has been transferred from a donor organism to a recipient cell by a virus

conjugation-new sequence

from plasmid exchange

energy acquisition (what and how)

phototrophs - obtain energy from light

autotrophs - require CO2 as a carbon source, can produce own food (producers)

chemotrophs - obtain energy from chemicals

heterotrophs - req. an org. nutrient to make organic compounds (consumers)

photosynthetic cells

heterocyst (large thick-walled cell found in filaments of certain blue-green algae and in certain fungi)

specialized bacterial cells that can fix nitrogen (a cell cannot fix nitrogen and photosynthesize in the same bubble)

biofilms

in some prokaryotic species, metabolic cooperation occurs in surface-coating colonies

(microorganisms share nutrients)

prokaryotic metabolism varies with respect to O2

obligate aerobes: req. O2 for cellular resp.

obligate anaerobes: poisoned by O2 and use fermentation or anaerobic resp.

facultative anerobes - can survive w/ or w/o O2

pathogenic bacteria

pathogenic prokaryotes typically cause disease by releasing toxins

• all known to date are bacteria (not archaea)

• cause about 50% of all human disease

• ex) mycobacterium tuberculosis, diarrheal disease, pest carried diseases